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M86-E00078 APEX2 User Manual.book

1. Figure 9 21 Isotropic refinement output In the output displayed above note that the R1 value is 0 08 This is typical for a preliminary iso tropic refinement for an organic molecule with data to a resolution of 0 75 and no hydrogen atoms included The refinement program also indicates that the model needs to be inverted to get the correct absolute structure NOTE This indication of the absolute configura tion is usually reliable but all assignments of absolute structure should be confirmed later in the refinement process by including TWIN and BASF cards in the instruction input Structure Solution and Refinement APEX2 User Manual 2 Click on OK to return to XShell The mole cule display will refresh with the results of the least squares calculations Figure 9 22 The model after isotropic refinement In the refinement box click on Invert Structure The peaks in the diagram represent difference and Refine All Non H Atoms Anisotropically as in the electron density between the refinement in Figure 9 23 model and the experimental electron density as m Sigma Cutoff nSigma defined by the measured data Many of these cates difference peaks are near the sulfur and oxygen A atoms Refinement of all atoms anisotropically Pee d should correct the model Figure 9 23 Inverting and choosing anisotropic refinement 9 16 M86 E000
2. Figure 9 24 Refine023 The value for R1 0 047 is typical for an initial anisotropic refinement with no hydrogen atoms included Since the mean shift esd is greater than 0 1 the model is still changing Since the highest peak in the difference map has a height of 0 49 and is 0 5A from C10 there are certainly some hydrogen atoms to be included M86 E00078 Structure Solution and Refinement Structure Solution and Refinement APEX2 User Manual Examination of the difference peaks in the resulting difference electron density map shows that the top difference peaks all correspond to hydrogen atoms Figure 9 25 Difference peaks correspond to expected hydrogen atom positions 9 18 M86 E00078 APEX2 User Manual Structure Solution and Refinement 9 3 4 Look at Atomic Displacement Parameters Thermal Ellipsoids It is generally good practice to examine the dis placement parameters at this point in structure determination 1 Remove difference peaks with the slider tool Figure 9 26 Removing all Q peaks with the slider bar 2 Right click on the background and select Thermal Ellipsoids Wireframe Ball And Stick Alternatively a list of Ueq s equivalent isotropic displacement parameters can be generated by requesting information on all of the atoms Figure 9 27 Selecting Thermal Ellipsoids Examining these values for outliers is good practice Figur
3. 6 18 2 M86 E00078 APEX2 User Manual Table of Contents 7 Data Integration and Scaling 7 1 7 AMIMCOTANON 2 oh bu Med epa 7 2 TAWACIVEWASK 7 8 8 7 94 mage QUOLlG ie ELS RS CERRO Ee oa a 7 8 7 2 Monitor the Integration Run with SaintChart 0 aaa aaa cc eee 7 9 7 2 1 Overall Rsym and Coverage Statistics 7 15 7 2 2 Unconstrained Unit Cell 7 16 Y DONC ee ioe gh Ora eG we 7 17 7 3 1 Setup Input Flles ette eu ee do ero op dee d det doe dee gees 7 17 7 3 2 Parameter Refinement 7 18 7 3 3 Error Model RETINGIMENTE d REDE dee od e WA A XN 7 19 7 34 Display DiaQnOSuCS ese acia dotar gor Ara acu o beens s Ra E Rio Sb 7 20 7 25 S Examine 8 1 SNP METUIT T TTE TERT sees 8 1 8 2 apace Group Delerminalilon trece eer n OD om eae cn CS o a ess 8 2 8 9 Reflection Statistics 5 eorr EG xU area wd d nda ee OC as oia RR RG 8 4 8 4 Applying High Resol
4. 2 8 2 VO COMDPUTErS 2 8 2 1 9 AC6OSSOLIOS inis DEP cuni oe ae E I LAS E us 2 8 3 Software Overview 3 1 9 1 The Server Computer 23 ac qur SR xU EROR E phe EUR Dod RR 3 2 3 1 1 Bruker Instrument Service 15 3 2 3 1 2 Bruker Control Program 3 2 3 1 3 APEX2 naer erai a ee 3 3 3 2 The Client CompulGer 3 ux oe ew m tea tad med es AE EM EE TRE Re qux ee ew ace 3 4 M86 E00078 1 Table of Contents APEX2 User Manual 3 2 1 Database and Database Connection 3 4 3 2 2 APEX2 eua iaa toe a nde a MR X 3 5 4 Program Start Up and Shutdown 4 1 4 1 Server Computer Start Up lilii 4 1 4 1 1 Starting Bruker Instrument Service BIS 4 1 4 1 2 Starting the APEX2 Server 0 cee eens 4 3 42 Chien Computer olalt DD enn Beene weds sue teed he Ex EE hee Gente du we pus 4 4 4 2 1 Starting th Database ss us Sass ten ete i i ac ed EU dr cod afe a e UR qu aad ENTER ase 4 4 42 2 APEX lane dos a Gor SEAS eu d eo eoo ob diet deir c a 4 4 4 3 Cli
5. 12948 2407 11 11 10 10 10 10 3 2 44 8 93 78 38 95 71 z9 03 TT 19 dI I 0 000 dI I 0 000 lt I gt Bg syn 17 3 4707 540 27 07 0 038 goes lt 5ig gt Bg Rss 21 5 7 0 amp 64 447 39 39 3 08 0 033 raw Se Sasi Shell Bsym Pairs Pairs BRshell 5iqma 0 032 l78 100 00 0 032 82 397 n 033 327 99 70 0 038 31 34 0 034 473 99 58 0 039 21 81 0 034 614 99 66 0 045 13 70 11 0 035 99 48 0 050 9 85 13 0 035 596 99 72 0 063 7 32 18 0 036 1051 99 52 0 076 4 84 28 0 03 1181 99 33 0 083 4 45 30 0 03 1313 39 47 0 098 3 34 40 0 038 1442 99 31 0 116 2 65 50 Figure 7 22 Final Saint Integration Statistics Add text M86 E000787 D e m om m J uu 05 06 04 22 32 31 Data Integration and Scaling Data Integration and Scaling APEX2 User Manual 7 2 2 Unconstrained Unit Cell Refinement Unconstrained global unit cell refinement 05 06 04 22 37 31 Performing final unit cell least squares on file d structurses idata for manualyylic Input file containz 5557 reflections Global Refinement single component data Maximum allowed reflections 2923 reflection will be stored in memory per 1 reflection s read Orientation least squares component 1 S552 input reflections Wavelength relative uncertainty O 7107300 0 0000089 Reflection Summary RLY Excl
6. Copy TE Paste F Clear Figure 6 22 UserManual014 bmp 3 Click Append Strategy APEX2 User Manual M86 E00078 APEX2 User Manual Data Collection 4 The program changes the name to the name of the current project in this example ylid_manual F sstruc gquest data_manual ylid_manual ylid_manual_01_0003 sfrm Setup Experiment Moritor Experiment Image location C struc quest ylid_manual Attenuate if topped Default time 10 000 sec frame Filename or prefix vid manual Correlate Frames Default width 0 500 degrees First Run 1 2 Generate new Dark Images Detector Format 512x512 Operation Active Distance mm 2Theta deg Omega deg Phi deg Chifdeg Time sec Widih deg Sweep deg Direction 4 1 PhiScan 35 000 22 000 285 99 358 39 3 83 5 00 050 36950 automatic 2 Omega Scan Yes 35 000 32 000 27 75 27 75 99 47 5 00 0 50 76 50 automatic 3 Omega Scan 35 000 7 000 26 26 26 26 55 59 5 00 0 50 37 00 automatic Phi Scan 40 000 28 000 14 91 14 91 34 09 5 00 0 50 81 automatic 5 No Operation Yes aes B Operation No Operation Yes No Operation Yes a No Operation Yes 10 No Operation Yes E No Operation Yes 12 No Operation Yes 13 No Operation Yes No Operation Yes 15 No Operation Yes 16 No Operation Yes 17 No Op
7. UKER BRUKER ADVANCED X RAY SOLUTIONS E APEX2 User Manual Version 1 22 USER MANUAL M86 E00078 7 04 PRELIMINARY UKER BRUKER ADVANCED X RAY SOLUTIONS APEX2 User Manual Version 1 22 M86 E00078 7 04 This manual covers the APEX2 software package To order additional copies of this publication request the part number shown at the bottom of the page 2004 Bruker AXS Inc All world rights reserved Notice The information in this publication is provided for reference only All information contained in this publi cation is believed to be correct and complete Bruker AXS Inc shall not be liable for errors contained herein nor for incidental or consequential damages in conjunction with the furnishing performance or use of this material All product specifications as well as the information contained in this publication are subject to change without notice This publication may contain or reference information and products protected by copyrights or patents and does not convey any license under the patent rights of Bruker AXS Inc nor the rights of others Bruker AXS Inc does not assume any liabilities arising out of any infringements of patents or other rights of third parties Bruker AXS Inc makes no warranty of any kind with regard to this material including but not limited to the implied warranties of merchantability and fitness for a particular purpose No part of this publication may be stored
8. GooF 5 Restrained Goof 1 064 for restraints Mean shift esd 0 000 Maximum 0 001 for OSF at 07 08 49 Max shift 0 000 for H11B Max dU 0 000 far C6 wRz 0 0808 before cycle 7 for 2430 data and 129 7 129 parameters GooF S 1 064 Restrained GooF 1 064 for 0 restraints Mean shift esd 0 000 Maximum 0 000 for OSF at 07 08 50 shift 0 000 for HLOB dU 0 000 for C11 wRe 0 0808 before cycle 8 for 2430 data and 129 7 129 parameters GooF S 1 064 Restrained GooF 1 064 for 0 restraints Mean shift esd 0 000 Maximum 0 000 for L11 51 at 07 08 50 shift 0 000 for H11C dU 0 000 far C11 wRz 0 0808 before cycle 9 for 2430 data and 2 129 parameters GooF S 1 064 Restrained GooF 1 064 for 0 restraints Ri 0 0296 for 2308 Fo 4sigfFo and 0 0315 for all 2450 data whe 0 0808 GooF S 1 064 Restrained GooF 1 064 for all data Ri 0 0307 for 1429 unique reflections after merging for Fourier Highest peak 0 25 at 0 2245 0 1515 0 2028 0 81 from C2 Deepest hole 0 16 at 0 0668 0 2087 0 2179 1 21 from C2 ylid resa75 finished at 07 08 50 Total CPU time 0 9 secs Figure 9 5 Initial view of the YLID molecule M86 E00078 9 5 Structure Solution and Refinement 4 Right click in the background to open a pop up window with
9. Index Spots Reduced Unit Select Spots For Indexing More Spots Resolution From 9999 00 Resolution 0 59 Spots Must Be Isolated Axis 10 000 B Axis 10 000 C Axis 10 000 Spots Must Span Images Spots Must Be whole Total Spots 259 Selected Spots 244 Indexed Spots n a Filter Tools Value 1000 0 3 Index CO 2 Harvested Images matrix ODUT sfrm E f Show Observed Spots Show Predicted Spots Figure 6 10 Indexing tool The defaults are usually OK Use the slider to omit reflections with lower l sigma from the cal culations If indexing is difficult try reducing the number of reflections used If indexing is difficult use the RLATT tool This tool is described in Appendix 2 Click on Index M86 E00078 Data Collection After approximately 30 seconds the index win dow will display a possible cell and the OK but ton will no longer be gray The values shown in Figure 6 11 are reasonable for the ylid Reduced Unit Cell wis 5 929 B 8 981 18 348 Alpha 29 955 Beta 99 811 Gamma 99 953 V alume 976 9 3 Figure 6 11 The unit cell The spot statistics are also acceptable with 98 i e 238 244 x100 of the selected spots indexed Total Spots 254 Selected Spots 244 Indexed Spots 230 Figure 6 12 Focus the spot results Ther
10. Is anothee postmaster 1788 running in data Figure 4 7 Database failure message 4 2 2 Starting APEX2 1a For Windows systems on the client com puter click on Start gt Programs gt Bruker Nonius Programs gt APEX2 or click on the APEX icon on the desktop 1b For Linux systems open a terminal window and type bnrun apex2 or click on the APEX2 icon M86 E00078 APEX2 User Manual 2 window will appear to login to the data base by entering a user and password see Figure 4 8 2 1 If the system manager has set up the system to automatically enter the user name and password step 2 is skipped Te 2 x User Password Cancel Figure 4 8 Login request 3 An empty start up window will appear see Figure 4 9 be Apex vi 0 20 User guest Ede Perum Wiecie cx Figure 4 9 APEX2 start up window M86 E00078 Program Start Up and Shutdown 4 Click on File Apex v1 0 File Instrument Lm Logout Mew i Open rau Figure 4 10 clickfile2 bmp 5 Use the options in this menu to create new project or to open an existing project 6 If the window in Figure 4 11 appears then APEX2 thinks the database is already in use Answer Yes to close the window ba Sample locked x i This sample is locked by another session Do you want to unlock the sample Figure 4 11 Sample Locked menu Program Sta
11. yellow Crystal Dimension 0 22 0 25 x 0 23 mm Crystal Shape Oblated sphere Figure 6 2 Describe window 6 Close this module The data will automati cally save to the database APEX2 User Manual M86 E00078 APEX2 User Manual 6 2 Determine the Unit Cell 6 2 1 Collect Images 1 Inthe task bar left click on Collect and then on Experiment Since there was no connection to the instrument when APEX2 was started the program recog nizes that it needs a connection in order to col lect images It will ask to connect see Figure a instrument Connection Host Name Figure 6 3 Instrument Connection window 2 Click on Connect 3 Click on Append Matrix Strategy at the bot tom left of the window M86 E00078 Data Collection Data Collection APEX2 User Manual Setup Experiment Monitor Experiment Image location C frames quest ylid_manual Attenuate if topped Default time 5 004 sec frame Filename or prefix matrix Correlate Frames Default width 0 500 degrees First Run fi Generate new Dark Images Detector Format 512x512 Operation __ Active Distance mm 2Theta deg Width deg Sweep deg Direction 1 Phi Scan Yes 40 000 30 000 45 000 0 000 54 740 default default 6 000 positive PhiScan Yes 40 000 30 000 45 000 120 000 54 740 default default 6 000 positive PhiScan Yes 40 000 30 000 45 000 240000 54 740 defaul default
12. Data Integration and Scaling APEX2 User Manual M86 8 Examine Data In this step the space group for the sample is determined and optional simulated precession photographs are calculated to further evaluate the overall quality of the data APEX2 provides two tools for this XPREP for space group deter mination and Precession Images for looking at undistorted slices of reciprocal space This is the final step before beginning the structure solution and refinement process M86 E00078 8 1 XPREP 1 Click on XPREP Space Group Determina tion under Examine in the task bar 2 Check that the two files in the pop up win dow are correct see Figure 8 1 and click OK file Jouest data_manual ylid_manual work ylid_manual_Om p4p HKL file Rguest data_manual ylid_manual work ylid_manual_Om hk Figure 8 1 Select files for XPREP input NOTE The scaling process has created two files ylid_manual_Om p4p containing the final unit cell parameters from integration and ylid manual Om hkl containing the corrected intensities Typically these are the files to use for Examine Data space group but you can browse to choose other files 8 2 Space Group Determination 1 XPREP evaluates the data and looks at the mean intensities and the mean int sigma Since these are large for all groups except P XPREP suggests that the lattice is P see Figure 8 2 Press Enter to accept t Bruke XPREP Ve
13. Resolution Cutoff 2 Theta Invert structure Late stage refinement options Refine all non H atoms anisotropically Use suggested weights Squared Term 6 000000 Linear Term Refine extinction parameter Generate ACTA CIF information file Refine Edit File Cancel Figure 9 20 The Refine menu M86 E00078 WR2 0 2818 before cycle 3for 2445 data and 57 57 parameters 2 496 Restrained GooF 2 496 for 0 restraints Mean shift esd 0 686 Maximum 2 456for y C11 at 11 50 43 Max shift 0 015 4 for C11 dU 0 001 for C2 wR2 0 2787 before cycle 4 for 2445 data 57 57 parameters GooF S 2 Restrained GooF 2 473 for D restraints Mean shift esd 0 180 Maximum 0 854 for y O2 at 11 50 44 Max shift 0 004 4 for O2 Max dU 0 000 for C4 WR2 0 2783 before cycle 5for 2445 data and 2 57 patameters GooF S 2470 Restrained GooF 2 470 for D restraints Ri 0 0879 for 2315 Fo gt 4sig Fo and 0 0918 for all 2445 data WR2 0 2783 GooF S 2 470 Restrained GooF 2 470 for all data Absolute structure probably wrong invert and repeat refinement Ri 0 0932 for 1440 unique reflections after merging for Fourier Highest peak 1 18 at 0 2500 0 3358 0 2419 0 51 from S1 Deepesthole 0 75 at 0 1606 0 2830 0 2403 0 51 Afrom S1 vlid res 5 finished at 11 50 44 Total CPU time 0 3 secs
14. Software Overview space group determination SaintChart output XShell refinement and Xcif report generation do not use the Task Display Area they open in a new window All other plug ins open in the Task Display Area of the GUI By ax ID c Setup Distance mm 37 50 Mosaicity 0 40 Image Width 0 33 Bijvoet Pairs merged Laue Class 1 Lattice Type Axis B Axis E Axis Evaluate Crystal Collect Completeness Experiment Oriented Scans Resolution Completeness Redundancy Completeness Aduepunpsy Integrate Examine Data Solve Structure Refine Structure Time h Instrument Figure 3 6 The Task Display area showing COSMO M86 E00078 Total Reflections Runs Req Disk Space Exposure Times s 67 7361 MB 07 2Theta 54 37 sintpA 1 4 055 Alpha Beta Gamma Unique Images Inf 1 37 0 71 0 504 0 41 0 37 0 364 M 0 160 0 0024 0 3644 0 7044 0 9974 1 2274 1 3674 1 4144 fio 4 4 4 30 E 30 4 Same Extend Reduce Reset Current Target Priority Completeness 99 52 fono 4 Redundancy 46 12 ong 5 Time h 1618 30 Strategy Execute Refine Strategy Software Overview APEX2 User Manual 3 10 M86 E00078 4 Program Start Up and Sh
15. A c struc guest data manual ylid manual lt z 0 matrix_O1_ work matrix_O1_ UFU HHH 1 12 02 s 1 12 E bn event log 3 matrix_O1_ EZ matris 03 t 1 12 E communication log 20040502 gz matrix_Ol_ vlid manual 01 ttti 1 739 E matis 01 0001 sfim 9 matrix_O1_ manual 02 stt 1 153 53 matrix 01 0002 sfrm a matrix 01 hii i 9 matis 01 0003 E mau manne PORE E matrix 1 O004 sfrm E matrix_02_ E matrix_01_0005 sfrm matrix 02 matrix 1 OODB sfrm matrix_02_ 2 Directory viia manual File type Directories Cancel 4 Figure 8 22 The simulated precession work area 2 open the file selection window left click on the folder beside the file name Choose the sets of images that you want to use for the calculation by clicking on the check boxes see Figure 8 23 M86 E00078 Examine Data bal python 2 Look in A c struc guest data manual ylid manual ter 8 T matrix_O1_ work matrix_O1_ 0 01 si 1 12 bn event log matrix_O1_ E E communication log 20040502 gz a matrix_Ol_ vlid manual 01 88 1 739 9 matris O1 QOC1 sfrm matrix_O1_ Ev 02 153 matrix_O1_ 0002 sfrm matrix_O1_ El ylid manual 03 1 74 matris 01 O003 sfrm matrix_
16. M86 E00078 Structure Solution and Refinement SORT ATOMS Sort Bin Atom List lt Top of List gt Sorti Alpha Mumeric Sorti Numeric Alpha Insert Selected After z Insert All Ofber gt lt Move Selected Atoms Sogt Bin lt Move All Atoms To Sort Bi Cancel Figure 9 32 refine2016 NOTE Generally it is easier to sort and number atoms before adding hydrogen atoms 2 Highlight the atoms to sorted i e left click and drag over the atoms and move them to the sort bin i e left click on Move Selected Atoms to Sort Bin Structure Solution and Refinement Sort Bin Sorki Alpha Numeric i Figure 9 33 refine2017 3 After the atoms are in the sort bin click on Sort Alpha Numeric to get them into a nor mal order APEX2 User Manual 4 Highlight O2 and click on Insert All After gt as in Figure 9 34 Sort Bin Atom List of List gt Sorti Alpha Mumeric Sorti Mumeric Alpha Insert Selected 4fter gt Insert All AfEer Figure 9 34 refine 2019 5 Click on OK to accept the sorting Figure 9 35 refine2011 M86 E00078 APEX2 User Manual The resulting list of atom information is easier to examine Fro a THFORMATION OH ALL ATOME B sl v Figure 9 36 Sorted atoms The Ueq are reasonable if there are e lower values for the sulfur atom and the five member ring e high
17. M86 E00078 2 1 APEX2 User Manual Hardware Overview APEX Il x LLI an lt Detector Power Supply p La zA oo 5 Qa c Controller c ru Q O Figure 2 2 SMART APEX II system Figure 2 1 Kappa APEX II system M86 E00078 APEX2 User Manual 2 1 1 APEX II Detector The APEX II detector is specific to this system Status lamps on the top of the detector housing indicate when the detector is on green and off red On Kappa APEX II systems the detector is mounted on a motorized 20 track The camera distance is computer controlled a typical dis tance for the camera is 40 or 50 mm On SMART APEX Il systems the detector is mounted on a 20 dovetail track The track has a scale that is calibrated in mm to indicate the dis tance from the crystal to the phosphor window a typical distance for the camera is 40 or 50 mm M86 E00078 Hardware Overview 2 1 2 Goniometer The goniometer module and APEX II detector comprise the unique hardware of the system This is the part of the instrument that actually performs the experiment Several components comprise the goniome ter module with APEX II detector e Goniometer 4 axis or 3 axis e APEX II detector e X ray source including shielded X ray tube X ray safety shutter and graphite crystal monochromator e 780 X ray generator e Timing shutter and incident beam collimator with beam stop e Video ca
18. me ESD 5 X 2 cepts X Y bean ceris Ditta comechorn Pech Mol Yaw comection v Coverage Statutes Harvested sefiectons Congietenen ond redundancy gon pus 3 etre 11 0 00 0 20 0 06 0 19 9 92 0 59 1669 9 11 0 09 19 0 69 0 71 0 60 1 000 etre 13 0 13 0 1 0 00 0 54 0 10 049 75 f 34 0 01 0 69 0 71 0 60 1 000 5 stra 12 0 26 0 19 0 97 945 0 10 1062 1 5 0 70 15 0 69 0 71 0 60 1 000 amp cfr 9 0 03 0 09 0 04 0 15 0 26 0 16 1292 2 0 78 24 0 69 0 71 0 60 1 000 7 s fem 14 0 04 0 08 0 07 0 54 0 15 0 24 9341 1 31 14 0 69 0 71 0 40 1 000 17 0 06 0 22 0 02 0 20 0 35 0 43 5251 2 17 48 0 74 a 0 6 0 71 0 60 4 000 Figure 7 17 SaintChart view M86 E000787 Data Integration and Scaling APEX2 User Manual As shown in Figure 7 17 when the SaintChart 1 2 Expand the windows to fill the available window opens the graphs are small and under graphical area by clicking on the four Linux the text area is large square icon in the upper right 1 Change the view BE 1 1 Change the text area by clicking and dragging on the line between the text and graphical areas EST LP ng 5 1 en on Components ace Spot Intensity and L Sigmew Conmpieieraz and iedundiancy ipo paz LE AT LB PrE 17 0 00 09 00 0 04 09 21 OL 1 8 0 73 0 62 0 55
19. 6 Click Refine Strategy 7 A list of options will appear Click on sort runs for completion Execute Refine Strategy Refine Strategy i Sort Runs for Completeness Figure 6 19 Choose Sort Runs for Completeness APEX2 User Manual y 100 80 5 e a 50 E 8 40 20 4 2 0 1 4 1 0 6 Resolution A Completeness Redundancy 100 80 re 8 a 50 e B gt 40 Q 4 20 2 0 Time h Figure 6 20 UserManual022 bmp M86 E00078 A uepunpaM APEX2 User Manual 8 Go to View gt Detailed Strategy The next window shows the runs to be collected Current Strategy 1 Strategy 35 00 2200 4288 99 358 39 3 83 Phi 738 26950 75 permanent 2 Strategy 35 00 32 00 24798 2775 99 47 153 76 50 75 Strategy 35 00 7 00 4 01 26 26 55 59 Omega agis 74 37 00 75 Strategy 3500 2800 485 14 91 34 09 Phi partal 162 81 00 75 1 E Figure 6 21 NOTE If for some reason it is necessary to start over change the distance slightly by 0 02 for example and press Return COSMO will reload all of the possible runs You are now ready to collect data M86 E00078 Data Collection Data Collection 6 4 Data Collection Run Experiment 1 Click Collect gt Experiment 2 Go back into the experiment window and delete the three matrix runs if they are still there First Aun 1
20. Orthorhombic 222 Tetragonal I P222 1 Rhombohedral F 2 1 1 Hexagonal C Porri Cubic Figure 7 3 Choosing P2 1 2 1 2 1 with the space group tool The resolution window on the upper right sets the upper resolution for integration Resolution Limit 0 750 Figure 7 4 The resolution tool The APEX2 Suite will suggest a resolution cut off In this case the suggested value changed to 0 75 M86 E000787 Data Integration and Scaling In the center of the bottom are two buttons for defining the data collection runs to be inte grated Find Runs Import Runs from Expetiment Figure 7 5 The Find and Import Runs buttons The import runs button determines the runs to be integrated from the experiment that has just been submitted Using this button allows the user to start integration while the data is still being collected NOTE SAINT will integrate all of the data cur rently measured and then will wait for the next image integrate that and wait for the next etc The Find Runs button is used to browse to the set of runs to be integrated The button is nor mally used when the data collection is finished Data Integration and Scaling 1 Click on Find Runs The following window will open usually it will have the correct directory and basename as the defaults If these are not correct then use the browse button to find the runs for the data col lection of inte
21. The Refine menu with histograms displayed M86 E00078 APEX2 User Manual Data Collection The YLID test crystal should have an orthor crystal should now be aligned so refinement of hombic primitive cell with approximate cell the crystal center is not necessary dimensions of a 5 95A b 9 03A c 18 38A and 90 2 Click View Histograms The histograms show how observed data compares to the data calculated using the current unit cell The HKL values should be close to integers and the rotation angle differences should not be significantly larger than the step size used to collect the matrix frames Click Refine several times Check the Constrain Distance and Con strain Beam Center boxes NOTE Check the constraints to fix the parame ters listed Uncheck the constraints to allow the parameters to refine 5 Uncheck Constrain Pitch Roll and Yaw Click Refine several times 7 Uncheck Constrain Distance and Constrain Beam Center and check Constrain Pitch Roll and Yaw 8 Click Refine several times NOTE In most cases the angle zeroes are close to zero and should not be refined The M86 E00078 6 11 Data Collection APEX2 User Manual 6 2 5 Determine the Bravais Lattice 1 After refining click Bravais Lattice and look for other unit cell choices i e look at fit val ues Choose Bravais Lattice ais A C B Arar Ses T Gammel voume c3 Orthorhombic 0 59 5 96
22. Vertical Beam Center mm 0 00 Image Header Tool Editar Cursor Position Figure 6 8 Image viewer with indexing tool M86 E00078 Data Collection Data Collection 2 The name of the first image is already entered Click on Harvest Spots NOTE All other options are gray at this point because there are no reflections available A blue progress bar will appear as the software determines the best background level to use for harvesting Then a window with two sliders will Fren Spots 1 lt Figure 6 9 Indexing sliders The right slider selects which image is dis played The left slider increases or decreases the 1 5 1 the cut off criteria for accepting reflec tions Generally the defaults are fine 3 Change the run number in the First Image box to matrix 02 0001 and click on Harvest Spots The run number is 02 The image or frame number is 0001 At this point you should have 100 to 300 reflec tions harvested APEX2 User Manual 4 Change the run number in the First Image box to matrix O3 0001 and click on Harvest Spots NOTE If run three is not completed a window will pop up that says Do you want to continue with the images that could be read If this hap pens skip step 3 and go to Section 6 2 3 Then return to Section 6 2 2 and harvest the spots before refining M86 E00078 APEX2 User Manual 6 2 3 Index the Reflections 1 Click on Index A window will open
23. are reflections excluded after cycle 1 because ELW error exceeded 0 0252 Component Input BLY Excl Used WorsthResz Best Res Min Max 1 5552 8 1065 0 7884 5 025 53 560 Orientation UB matrix 0 0584509 O 0333484 0 0485062 0 00053298 O 1049404 0175150 O 1573566 0 0121009 0 0180036 E C Alpha Beta Ganna Vol 5 9572 0273 15 3669 30 086 59 999 30 033 0 0001 0 0002 0 0004 0 001 0 001 0 001 0 05 Corrected for goodness of fit 0 0005 0 0008 0 0019 0 005 0 005 0 005 0 22 Figure 7 23 Unconstrained unit cell refinement Check the angles in the unconstrained unit cell refinement to get a quick confirmation that the initial lattice determination was correct In the unconstrained refinement angles that are required to be 90 or 120 are allowed to refine If they differ considerably from the expected value then the data should be checked carefully 7 16 M86 APEX2 User Manual 7 3 Scale The scaling process uses the SADABS program to put all of the measured data on the same scale This process involves five steps 1 Setup input files Parameter refinement Error model refinement 2 3 4 Display diagnostics 5 Exit 7 3 1 Setup Input Files 1 Click on Scale gt Scale in the task bar Fig ure 7 24 shows a portion of the initial Scale work area The defaults and file names are typically correct Base pid manu 7 Output hkl file id mand Diagnostic Plot
24. see Figure 8 12 Examine the data presented 1 the completion near 100 Is the redundancy good Are Rint and Rsigma small and increasing smoothly from top to bottom In particular look at the last two lines which compares all of the data with the high reso lution data The completion should be near 100 for both the high resolution shell and the complete data set The redundancy and Rint should be similar for the two The Mean Intensity and the Mean l sigma l will usually be quite different The Mean l sigma l for the high resolution data should be greater than 3 0 M86 E00078 APEX2 User Manual For this data set the difference between the Rint for the high resolution data and the complete data set is slightly larger than expected Press Enter to continue XPREP Ver 6 14 W95 98 NT 2000 ME Copyright Bruke Resolution Data Theory Complete Redundancy Mean I Mean I s Rint Figure 8 12 Intensity statistics 5 Since the difference between the Rint for the high resolution data and the complete data set is slightly larger than expected it is reasonable to apply a high resolution cutoff using the H option in the data manipulation menu see Figure 8 13 Type H and press Enter Figure 8 13 Requesting a high resolution cutoff M86 E00078 Examine Data 8 4 Applying High Resolution Cutoff 1 Entera high resolution limit of 0 75 see Fig ure 8 14 and press Enter to accept the low resolution cu
25. 1 000 i nire 11 0 123 0 02 40 33 9 9 EZ 0 73 D 3 d 55 1 D00 F ER 5 J gF s 03 0 06 0 IF z 1 8 0 73 0 62 0 55 1 00 F ER B 0 05 0 00 0 1 09 16 9 10 IHE 3 E gF EL 0 73 D 3 d 1 D00 0 04 0 06 EF 0 231 0 13 0 17 1246 6 1 0 31 17 0 73 0 09 d 1 D00 onnected F Integration in F ER 0 02 014 d 0 2 0 34 OLF 2001 8 15 11 0 91 19 30 73 2 68 1 D00 Figure 7 18 SaintChart view with graphical area expanded 7 10 M86 APEX2 User Manual To the left of the graphical area are a series of check boxes that select the displays 1 Add other displays 1 1 Click on integration progress to add the new display seen in Figure 7 19 When the integration is complete the blue progress bars will be full and the remaining time will be zero Integration Progress 584 739 BEEN 0 153 D 4 0 161 684 1127 vid manual OOCT sfrm vid manual 02 OUCT sfrm uid manual 03 OUCT sfrm vid manual ODCT sfrm All 22 25 20 00 00 24 22 28 08 00 03 05 22 30 13 00 05 09 22 32 96 00 07 53 22 32 96 00 07 53 Figure 7 19 Integration progress display M86 E000787 Data Integration and Scaling Data Integration and Scaling One of the most powerful windows for monitor ing the progress of the integration is Spot Posi tion Overlay in Per Image Statistics Pull up on the Window Tool Bar for
26. 3 0 High resolution threshold 0 1 Factor g for initial weighting scheme 0 04 Restraint esd for scale factors 0 002 Absorption Weak Absorber m Number of refinement cycles 50 Finish Start Over Exit amp XScale APEX2 User Manual M86 APEX2 User Manual 7 3 3 Error Model Refinement Figure 7 26 shows typical Error Model results ratini Find puc cartis Total fat F Total 12545 X Resecied 01 naan 085 Bu 1 08 06 Inckude the boksing bahchea Humber of Reflections 220 Figure 7 26 Error model results NOTE If the R values are significantly higher than this step repeat the entire scaling calcula tion Click the check box by the bad run and then click Repeat Parameter Refinement M86 E000787 Fipan Hafi teeth teres i1 ee ratio dor 40 fion m 1 Ere Suggested Use c Latches Rina incid esos rig 00302 0092 0921 0901 104 0471 0734 pedi LUGS OF 0530 345 1552 DEN TEh2 7455 0015 0097 098 DUE 1007 0558 oo 00055 DATI QF 345 1043 Oden 1515 1453 Determine Model Parameter Refinement Data Integration and Scaling Data Integration and Scaling APEX2 User Manual 7 3 4 Display Diagnostics 1 Click Finis
27. 5 000 positive No Operation Yes 5 No Operation Yes e No Operation Yes T Em No Operation Yes No Operation lYes a No Operation Yes No Operation Yes No peration Yes No Operation Yes No Operation Yes No Operation Yes 15 No Operation Yes 16 No Operation Yes 17 No Operation Yes M Append Strategy Append Matrix Strategy Validate Execute Resume Figure 6 4 Append matrix runs NOTE Adjust the time upper right to match the 1 Adjust the scan time and scan width if P scattering ability of the crystal e g shorter desired The default values are usually times for strong diffractors and longer exposure good The default time of 10 seconds is times for weak diffractors If the exposure times acceptable for most samples but shorter are five seconds or less click on the check mark times will not adversely affect most experi by Correlate Frames to turn off this feature ments Frame correlation measures each frame twice 2 Click on Execute Resume The view will at typically 1 2 the time and then combines the shift to the Monitor Experiment view see two together This is usually not necessary with Figure 6 5 The program will collect a shorter exposure times series of three runs with twelve frames per run This typically takes less than ten min utes
28. 55 Positioned labels 6 Convert this image into a high quality jpeg for inclusion into reports by clicking on ren der in the Windows Tool Bar and choosing Black and White to High Quality JPEG file Constrain Model Render Preferences Help To Screen I Black and White To Printer Figure 9 56 Generate JPEG HighGQuality JPEG File 9 28 APEX2 User Manual NOTE A message may appear that the font file needs to be defined Please set your font direc tory for the first time for opengl rendering If this happens click on Preferences OpenGL Pref erences Then click on the true type font For OpenGL In Windows browse to C bn xshell fonts or in Linux go to usr local bin xshell fonts Choose a font M86 E00078 APEX2 User Manual XShell 6 2 c struc quest data_manual ylid_manual work ylid_reso6 res 2 9 Figure 9 57 The final rendered thermal ellipsoid atomic displacement parameter plot M86 E00078 Structure Solution and Refinement Structure Solution and Refinement APEX2 User Manual 9 30 M86 E00078 Appendix A SAINTPLUS Occasionally it is necessary to integrate images outside of the APEX2 GUI Usually this is nec essary in order to import a matrix p4p file SaintPlus executed from a command window is designed for this purpose 1 Open a Command Prompt window 2 Change directories to the folder of interest 3 ForWindo
29. Integrated Spots the cursor arrow is pointing to this tool bar in Figure 7 20 to display the entire window see Figure 7 21 O Scan 3 Integration 35 00 All Components Progress Statistics 30 00 Integration progress Per Image Statistics Spot shape correlation 14000 00 4 12000 00 10000 00 Spot intensity and 1751 vl 25 00 E O Spot intensity lt 2 Sigmaf l 0 72 8000 00 Number of reflections harvested 6000 00 Spot position overlay A Y Z error PD X Y Z RMS difference 15 00 oO x Y Z spot size oO Queue extent used Primary beam intensity 10 00 Periodic Statistics LE Profile snapshots RD axis ESD C axis ESD Image D axis ESD Intensity sigma Alpha angle ESD Beta angle ESD O Gamma angle ESD Cel volume ESD C LS goodness of fit LS Residuals O A Y Z crystal translation X Y beam center Distance correction O Pitch Roll Yaw correction if Angle zeros Coverage Statistics Harvested reflections Completeness and redundancy V Bijvoet pairs S 8 4000 00 Average spot intensity 2000 00 0 00 APEX2 User Manual M86 APEX2 User Manual In this full view the Integrated Spots window looks much like the image viewer used previ ously but there are no tools At the bottom of the window is an entry box that can b
30. Z axis Lock counting Co i UTE Z axis Adjustment o Screw Y axis Lock Y avis Adjustment Screw x axis Adjustment Screw X axis Lock X axis Lack Figure 5 8 Huber goniometer head in detail 5 6 M86 E00078 APEX2 User Manual Crystal Orientation YLID Crysal Sample Mounting Screw d Sample Mounting Collar Z axis Adjustment Screw Y axis Lock Y axis Adjustment Screw X axis Adjustment Screw X axis Lock Figure 5 9 Standard goniometer head in detail M86 E00078 5 7 Crystal Orientation APEX2 User Manual 5 8 M86 E00078 6 Data Collection The data collection process is carried out on the client computer using APEX2 Once data collec tion is started exit APEX2 Data collection will continue M86 E00078 6 1 Start a New Project and Describe the Sample 1 Left click on File New 2 Inthe window that appears enter the sample name bg New Sample Mame Template Folder Mrames questylid manual pe Figure 6 1 The New Sample window 3 Click OK 4 The task bar will appear with the Setup sec tion open Left click on Describe Data Collection 5 Enter the requested information into the Describe window Setup Describe Center Crystal Name manual Compound rest ylid for manual Formula H10 02 51 Appearance Intensity Primary Color Secondary Color Crystal Color translucent pale green
31. and scales to make centering and measuring the crystal easy 2 1 4 K780 X ray Generator The K780 X ray generator is a high frequency solid state X ray generator which provides a stable source of power for operations up to 60 kilovolts kV and 50 milliamps mA For the APEX system power settings should never exceed the maximum power rating of the X ray tube Typical maximum power settings for the APEX II system with a fine focus tube are 50 kV 40 mA For both types of tubes the kV setting should not exceed 50 kV and the power kV x mA should not exceed the rating given on the tube cap This generator is interfaced to the controller and the power settings can be adjusted within the APEX2 software This is usually not necessary though as the software automatically increases the power to the user defined values at the beginning of an experiment and lowers them when the instrument is inactive M86 E00078 Hardware Overview 2 1 5 Radiation Safety Enclosure with Interlocks and Warning Lights A common component of all systems in the D8 family is the radiation safety enclosure This new design is fully leaded leaded metal sides and panels leaded windows to protect you from stray radiation The enclosure also includes warning lamps a government requirement that alert you when X rays are being generated And as a special feature the enclosure incorpo rates interlocks for both hardware and soft ware an automatic s
32. better with high redundancy in a reasonable amount of time When COSMO is first started it will tell you the completion redundancy and time for all of the available runs It is almost M86 E00078 APEX2 User Manual never necessary to let COSMO run to comple tion Typically it should be stopped when com pletion is greater than 99 and the time is close to what is desired M86 E00078 Data Collection 100 co e Completeness 50 0 1 4 1 2 1 0 8 Resolution Completeness amp Redundancy o Time h Figure 6 17 Completeness and redundancy chart 16 14 12 2 10 amp 0 3 o lt 4 2 10 a A 5 b m o lt 4 2 Data Collection In this example as shown in Figure 6 18 the completion is 99 76 and the time is approxi mately 2 33 hours NOTE Time estimates are approximate They depend on the number of rescans general instrument overhead backlash compensation etc If estimated times are consistently longer or shorter modify the COSMO hardwire profile 5 Click Stop when the completeness nears 100 and the time and redundancy approach the desired values It is not neces sary to wait until the refinement reaches 100 Current Target Priority 99 76 00 00 100 7 48 50 00 5 zi na E ea n3 ce e L ea Best in 2 hours Figure 6 18 Strategy status and priority control
33. button to the right of the Ele 3 Right click to view a pop up menu and ment field This will open a periodic table select Labelling Left click on the appropriate element sym bol to select it the periodic table will auto ud matically close p Show Labels Show Hydrogen Labels Sains Plane Weighted Plane Associate Connected Atoms Grow Move to Symmetry Equivalent Site Pack en Constrain Model Add hydrogen atoms Figure 9 13 New background color Figure 9 14 Select Labelling M86 E00078 9 11 APEX2 User Manual Structure Solution and Refinement 15 m i a Figure 9 16 Refine014 5 Once the element type is set correctly click on Relabel to number the peaks sequen tially in the order they were selected starting with the number in the First Sequence field M86 E00078 9 12 APEX2 User Manual 6 Seeing the color of atoms can be difficult in the Wireframe view used so far Right click in the background with no atoms selected to get a slightly different action menu In this menu highlight and left click on Pipes This m Hydrogen Labels Wireframe Ball And Stick Thermal Ellipsoid Select atkms Hide Part s Shaw all 4toms Structure Solution and Refinement makes the bonds thicker and makes it obvi ous that there is an incorrectly labeled atom That will be corrected when the carbon atoms are labeled Disassociate Atoms Unit
34. cutoff see Figure 8 19 Press Enter to accept Current dataset Wave length Uriginal cell Esds Current cell Matrix Crystal system E Formula Formula wt Density At vol 000 Mu 1 1 Figure 8 19 Changing the file name 5 After entering the file name or hitting return to accept the default file name an input file for the structure solution module is created and displayed on the screen And the pro gram asks Do you wish to over write the intensity data file ylid_res75 hkl Since the file name has been changed this question must be answered with a y see Figure 8 20 APEX2 User Manual Figure 8 20 The input file for structure solution and a final question 6 Exit XPREP see Figure 8 21 Press Enter to exit the program X Figure 8 21 Exit XPREP from the general menu NOTE There are many other features in XPREP that can be accessed from the general menu reciprocal space plots simulated powder patterns and a test for merohedral twinning are very useful tools M86 E00078 APEX2 User Manual 8 6 Simulated Precession Images 1 Click on Precession Images under Examine in the task bar Precession Images provide an undistorted view of layers of the recipro cal lattice APEX2 generates simulated pre cession images by finding the appropriate pixels a series of sfrm images You must specify the images to examine and the zones to calculate 21x Look in
35. on the server com puter Crystal Orientation 5 1 Mount the Goniometer Head on the Instrument N CAUTION Use extreme care when handling the goniometer head to prevent damage to your sample on the end of the small glass fiber 1 Open the enclosure doors Push either of the rectangular green Open Door buttons on the side posts This will release the door locks for approximately five seconds During this time pull out on one or both of the han dles to physically open the doors 2 Inthe APEX2 Server GUI under Setup click on Center Crystal The centering buttons will appear and the video window will open Center Crystal E f Manual Y Motorized Spin Phi 30 Spin Phi 180 Mount Lett Right Figure 5 1 APEX2 User Manual The bottom five buttons will drive the goniometer to various predefined positions that are designed to simplify crystal centering The top two buttons will drive phi by either 90 or 180 degrees 3 Click on Mount to mount an empty goniome ter head and determine the position NOTE On Kappa APEX II systems in the mount position the key or pin on the mounting base will be toward the back of the instrument On SMART APEX II systems at 0 the key on the mounting base of the goniometer head will be at the 12 00 position A CAUTION Use extreme care when handling the goniometer head to prevent damage to the sample on the end of the small glass fiber 4 Car
36. proven and widely accepted programs used by these modules e g SAINT SADABS XPREP XS XM XL etc underlie the GUI and provide powerful tools From a hardware viewpoint APEX Il systems share common hardware components with other Introduction Bruker products Other members of this new generation of instruments include the 08 ADVANCE and D8 DISCOVER and the D8 GADDS systems for general diffraction Docu mentation on some of these common hardware and software components is available in the user s manuals for the D8 family of instruments APEX2 User Manual 1 2 User Manual Features This user manual and associated YLID test data are intended to provide you with a step by step guide to data collection and processing using the APEX2 software program The test data supplied was collected on an X8 or Kappa per Ludger diffractometer with an APEX II camera and graphite monochromated molybdenum radiation from a sealed tube gen erator The high quality data resolution 0 75 A allows easy refinement of the hydrogen atom positions and determination of the absolute structure of the sample NOTE Before using this manual check that your system is in proper working order e g the optics and goniometer are aligned and that the APEX2 suite is properly installed M86 E00078 APEX2 User Manual 1 3 X ray Safety X ray equipment produces potentially harmful radiation and can be dangerous to anyone in the immediate vic
37. 02_ EZ vid manua 04 888 1 161 matris Q1 O004 sfrm matrix_02_ matris 01 OOD5 sfrm matrix_02_ matris 1 OODB sfrm matrix_02_ gt Directory vlid manual Filetype Directories Cancel Figure 8 23 File Selection window with matrix runs deselected Check the default input value Modify as needed and press Calculate Calculating more zones does not significantly increase the calculation time In the example 1kl and hk1 have been added to the defaults of and Fractional values e g 0 5kl are allowed Reducing the resolu tion may speed the calculations slightly The thickness defines the range of pixels above and below the requested range For example if the Okl zone is requested with a thickness of O 1 then the simulation is looking for all pixels that have 0 1 h 0 1 and any value including frac tional values for k and l Examine Data APEX2 User Manual Planes oki hBl hkD TEI hil Images from ruc guest data manual ylid manual 1127 image files in 4 runs best resolution 0 77 Thickness 0 10 Calculate Created files Figure 8 24 Detail of the input section 4 A progress bar will appear and after approx imately 5 10 minutes depending on the number of sfrm files read an image will appear on the screen Display other planes by clicking on the calculated images to the bottom right of the work area or by brow
38. 1 Examine SAINT text output At the bottom of the SaintChart window is a scrolling text window that displays the text out put from Saint This window can be expanded by dragging the horizontal bar above the text as indicated by the arrow in Figure 7 22 2 Examine the final results At the end of the integration examine this text critically In particular look at the Overall Rsym the coverage statistics and the unconstrained unit cell refinement For a typical small molecule structure the over all Rsym is usually less than 8 Higher values may indicate problems with absorption twinning or poor crystal quality APEX2 User Manual M86 APEX2 User Manual 7 2 1 Overall Rsym and Coverage Statistics in a r un 5 pe D Cj E D mA ES UN a Lx 1 00 coefficient Coverage Statistics for ylid manual On 0 80 eb nau Overall l 000 nau Centric l 000 000 4ngetrmus to 1 615 to 1 282 to 1 120 to 1 018 to 0 945 to 0 889 to 0 8465 to 0 808 to 0 777 to 0 750 12956 2413 Pairs 1442 Pairs 447 Uri l miq 451 454 Obs Theory tCompl LS 327 473 614 TEQ 1033 1183 L317 1451 Averaged local Local refinement results for component 1 175 100 99 475 99 616 99 763 99 903 99 1036 99 1189 99 1320 99 1452 99 cell least squares refinement 00 70 58 B8 61 34 71 50 UU
39. 2 Client Computer Start Up On the client computer two programs are also required the database and 2 It is best to start the database before starting APEX2 NOTE For the SMART APEX II there is typi cally only one computer for the client and server software 4 2 1 Starting the Database 1a For Windows systems click on Start Pro grams Bruker AXS Programs Start Database or click on the Start Database icon on the desktop d 16 For Linux systems open a terminal window and type bnrun startdb or click on the Start Database icon A window should appear that says the database system is ready Start Database database system was interrupted at 2004 04 30 15 04 38 CDT checkpoint record is at 0 32 75000 redo record is at 073275000 undo record is at shutdown FALSE gt next transaction id 669 next oid 83108 database system was not properly shut down automatic recovery in progre ReadRecord record with zero length at 073275040 redo is not require database system is ready Figure 4 6 The database is ready You can minimize this window If the database has not previously been closed properly e g APEX2 User Manual after a power failure a window will appear see Figure 4 7 that states that another postmaster is running If this happens stop the database and then start it again Start Database 1 already exists
40. 2 User Manual 4 4 Server Computer Shutdown Stop APEX2 Server before BIS It is ok if the order is inverted Generally BIS is never stopped 4 4 1 Stopping the APEX2 Server 1 Click on the X in the upper right corner of the window or click on File Exit in the upper left It is not necessary to disconnect from the instrument 4 4 2 Stopping BIS It is almost never necessary to stop and exit BIS If necessary click on the stop BIS button on the bottom of the BIS window and then click on the exit button at the bottom of the window M86 E00078 Program Start Up and Shutdown Program Start Up and Shutdown APEX2 User Manual M86 E00078 5 Crystal Orientation We are now ready to begin data collection with the instrument using the YLID test crystal We assume that your system manager has set up the system properly and that all system default parameters have been set appropriately The data collection process is divided into five steps See Section 5 1 Centering aligning on the diffractometer from the APEX2 Server the center mod ule M86 E00078 2 Crystal quality check from the APEX2 Server the simple scans module See Section 6 3 Cell determination from APEX2 the cell determination module 4 Data collection setup from APEX2 the strategy module 5 Data collection from APEX2 the experi ment module The first steps mounting aligning and screen ing a crystal are performed
41. 244 sp3 0 0 05 12 foun 104 8200Q 0 2908 0 615 0 380 523 0 0 05 1 98 8900 0 4789 0 856 0 93 sp3 0 0 05 14 013 85 8200 0 6561 0 1836 0 3232 5 0 0 05 15 014 66 1600 0 5674 0 1814 0 23955 3 0 0 05 16 015 64 7300 0 8062 0 4621 0 2409 5 0 0 05 17 916 54 7300 0 9493 0 1856 0 1563 5 0 0 05 ae 40 2200 0 52 0 989 0 237 5 0 0 05 Print Figure 9 7 Atom information screen At the bottom left of this window is a slide bar which is used for deselecting peaks The arrow can be moved by left clicking and dragging the arrow or by left clicking on either side of the arrow Left clicking to the left of the arrow i e where the cursor is pointed in Figure 9 8 will remove peaks M86 E00078 Fesidual Difference Fourier Q Peaks 0 Mo of QPeakz 22 Figure 9 8 The Q peak slider 5 Slide the pointer down while watching the molecular display Change the number of Q peaks to 15 Structure Solution and Refinement APEX2 User Manual At 15 the molecule is much cleaner but there 6 Put the cursor over the bonds to check dis are still peaks that do not make sense tance The distance will be displayed at the bottom right The distance of 1 178 is typi cal for C 0 in aromatized ring systems Figure 9 9 Image after the number of Q peaks was changed to 15 Two more clicks left on the Q peak slider gives a reasonable model X Figure 9 10 Image with
42. 5 Observed in 1 1 1 2A Shell Method E v Structure Expansion Computing Effort log scale t Solve Structure STOP Reset Exit Figure 9 1 Default Solve Structure view M86 E00078 APEX2 User Manual 2 Click on Solve Structure to start the calcula tions and open an output window This win dow can be used to monitor the progress of the direct methods calculations u Structure Solution Log Window 172 Reflections and 3346 unique TPA for R alpha 465 Unique negative quartets found 465 used for phase refinement 110 Unique employed in phase annealing 128 Parallel refinements highest memory 3822 44055 Ralpha Mqual Sigma 1 M abs Semirreariants 1830781 0 064 0 770 0 946 1 154 0 064 Freq OOO SF 1300000000100101001001211112125 317713 0 060 0 799 0 946 1 151 0 060 Freg 01 201 22 00000000100101221001222112 256 256 Phase sets refined bestis code 917713 with CFOM 0 0537 Fourier and peaksearch HE 0 154 for 14 atoms and 467 E values Fourier and peaksearch HE 0 140 for 14 atoms and 467 E values Fourier and peaksearch reso 5 finished at 0 46 22 Total elapsed time 0 9 secs Figure 9 2 Structure Solution output 3 Clic
43. 78 APEX2 User Manual 3 Click on the Refine button to launch the least squares refinement program The out put window will open and a summary of the results of individual cycles of refinement will appear GooF S 1 627 Restrained GooF 1 627 for 0O restraints Mean shift esd 1 801 Maximum 15 000 for U13 51 at 11 52 34 shift 0 010 for C5 Max dU 0 004 for C5 wR2 0 1427 before cycle 3for 2445 data 127 127 parameters GooF S 1 Restrained GooF 1 257 for D restraints Mean shift esd 0 503 Maximum 2 462 for U13 51 at 11 52 34 Max shift 2 0 005 4 for C5 Max dU 0 002 for C6 wR2 0 1408 before cycle 4 for 2445 data 127 127 parameters GooF S 1 236 Restrained GooF 1 236 for D restraints Mean shift esd 0 095 Maximum 0 561 for 033 C6 at 11 52 34 Max shift 0 001 for dU 0 000 for C5 wR2 0 1407 before cycle 5 for 2445 data and 2 127 parameters 1 233 Restrained GooF 1 233 for D restraints Ri 0 0468 for 2315 Fo gt 4sig Fo and 0 0489 for all 2445 data wR2 0 1407 GooF 1 233 Restrained GooF 1 233 for all data Ri 0 0505 for 1440 unique reflections after merging for Fourier Highest peak 0 49 at 0 8141 0 0816 0 2288 0 95 Afrom C10 Deepest hole 0 24 at 0 6815 0 3980 0 1149 1 21 from wlid res75 finished at 11 52 34 Total CPU time 0 5 secs
44. 9 04 18 42 99 94 83 37 99 90 992 ep ss 3 6 5 x Cancel Figure 6 14 Bravais lattice display Now you have a unit cell ready for determining a data collection strategy Note that even though monoclinic has a slightly better fit the software makes the correct choice of the higher symmetry cell 2 Click on the appropriate Bravais Lattice in this case orthorhombic 3 Press OK to accept the suggested lattice settings 4 Refine again Hefine for several more cycles changing the constraints one or two at a time 6 12 M86 E00078 APEX2 User Manual 6 3 Determine the Data Collection Strategy APEX2 includes a powerful algorithm COSMO for determining an efficient strategy that fully uti lizes the flexibility of your instrument 1 Left click on Collect gt Data Collection Strat egy if Y il ll Figure 6 15 The strategy display Refine Strategy M86 E00078 Data Collection Data Collection NOTE COSMO will use information from cell determination to set defaults You can modify the suggested values How 2 Check the inputs for defining the data col lection 2 1 Set the data collection distance For SMART APEX II systems this should be set to the actual detector distance For Kappa APEX II systems there is a vari able DX and the distance will default to the shortest reasonable distance Generally for the APEX II detector t
45. Cell m Labels Figure 9 17 Choose the pipes view 7 Left click on the remaining peaks in the order that you want them labeled NOTE If working on the YLID test data look at Figure 9 18 and click on the peaks to give the same order as used here Right click and choose Labelling Select Carbon and apply the labels M86 E00078 Zoom Cu Toggle Pan 4nd Rotate Restore Deleted Atoms Find Duplicate Labels 9 10 In the labelling tool change the el type to C carbon The starting atom number will change to 1 the first available number for carbon atoms Click Relabel Click Cancel to close the window Structure Solution and Refinement APEX2 User Manual 9 3 3 Refine the Molecule The labeled ylid molecule is now ready for refinement Figure 9 18 Correctly labeled model 1 Left click on the Refine icon in the tool bar the cursor is pointing to it in Figure 9 19 or Type Control R Figure 9 19 The Refine icon 9 14 M86 E00078 APEX2 User Manual Structure Solution and Refinement After a few seconds a Refine window will open with output results for the calculation This will open the Refine Box Click on Refine to launch the least squares refinement program XL using the default parameters as given REFINE Least squares options Full Matrix Conjugate Gradient Refinement Cycles Number of residual peaks zo Sigma Cutoff Sigma
46. Integration and Scaling Data Integration and Scaling APEX2 User Manual Figure 7 32 shows a single plot so that the dots expected This kind of problem may affect the are easier to see Note that the points of dis final results agreement are spread fairly evenly over the Scan L detector 2 theta 12 00 1 15 gt 3 00su red blue errors black entire detector face T Y Y 7 Cages o Spatial distribution of l el su for ylid_manual Sean detector ithe 22 00 Asl 23 0080 neds blue h errors black 50 150 200 250 300 350 400 450 N gt Figure 7 33 A Spatial Distribution plot showing a problem area i loic Graha A Fielnemeni Grech Ens Model Gusti A Soole Vanobona Intenst Figure 7 32 A single Spatial Distribution If the spots are clustered in an area or if there are significantly more spots of one color than there are of another then the data should be examined critically Figure 7 33 is from another data set where the active mask was not used during integration and the reflections collected in that area are consistently smaller than 7 24 M86 APEX2 User Manual 7 3 5 Exit 1 Click on Exit XScale to close the scaling GUI Exit AXS cal Figure 7 34 Exit XScale NOTE Scale is one of the few GUls where it is necessary to exit using a special exit button This avoids an error message that SADABS has exited improperly M86 E000787 Data Integration and Scaling
47. Introduction 1 1 APEX Il Systems for Chemical Crystallography Bruker AXS Kappa APEX II and SMART APEX systems are the newest members in the Bruker Nonius product line of instrumentation for single crystal X ray diffraction The systems provide the tools for complete small molecule structure determination The hardware and soft ware are completely redesigned The software features a new start to finish graphical user interface GUI The hardware features a new CCD detector based upon four port readout of a 4K chip and a choice of two goniometers APEX systems are enclosed in a fail safe X ray enclosure system The Kappa APEX II system features the Kappa 4 axis goniometer Two computers are used for experiments One computer the server controls the goniometer The other computer the client M86 E00078 controls all other aspects of the experiment from data collection through report generation The SMART APEX II system is an enhanced version of the SMART APEX fixed chi system A single computer controls the data collection and solution and refinement of the structure From a software and operational viewpoint the APEX II systems use the GUI of the APEX2 software suite to control all operations from crystal screening to report generation for a typi cal crystallography study This is a complete departure from the command driven function ally separate modules of SMART SAINTPLUS and SHELXTL Enhanced versions of the
48. S 0 475 Restrained Goof 0 475 for D restraints Ri 0 0284 for 2315 Fo gt 4sig Fo and 0 0303 for all 45 data wR2 0 0781 0 475 Restrained Goof 475 for all data Ri 0 0291 for 1440 unique reflections after merging for Fourier Highest peak 0 25 at 0 7757 0 3500 0 2034 0 81 from C2 Deepest hole 0 16 at 0 1920 0 4763 0 0236 1 29 A from C6 wlid res75 finished at 11 53 17 Total CPU time 0 5 secs Figure 9 42 Refinement results The value for R1 0 029 is typical for an aniso tropic refinement with riding hydrogen atoms and a data set measured to 0 75A Since the mean shift esd is less than 0 01 the model is not changing significantly Since the highest peak and the deepest hole in the difference map are similar there are probably no missing atoms The resulting difference electron density map appears rather ugly This is because the number of difference peaks to be displayed has been left at 20 M86 E00078 Structure Solution and Refinement Figure 9 43 Difference peaks in a well refined model 9 3 7 Final Refinement for Publication 1 Forthe final cycles of refinement reduce the number of peaks to be displayed to five and turn on Use Suggested Weights and Gener ate ACTA CIF Information File as shown in the next two figures NOTE If the sugges
49. The images will stop changing when NOTE The format for frame names is shown in the experiment is done Figure 6 5 Every frame is assigned a name For this figure the name is ylid manual 01 005 sfrm This means that the 6 4 M86 E00078 APEX2 User Manual frame is for the project ylid_manual and that this is the fifth image of the first run eApex2 1 0 20 User guest File ylid_manual Experiment 3 File Instrument Windows 8 XI JB c 81 mnm Collect Left and right Up and down arrows move arrows move Data Collection between frames between runs Strategy Experiment Oriented Scans N UOO ene em dore oet tcd 10 100 1000 10000 100000 1000000 Integrate Examine Data Distance 35 00 2Theta 338 00 Omega 286 99 Phi 3 61 Chi 3 8 Solve Structure it Distance 35 00 2Theta 338 00 Omega 286 99 Phi 4 11 Chi 3 8 Refine Structure Instrument Figure 6 5 Monitor Experiment view M86 E00078 Data Collection Data Collection To change the color of the image display e g Black on White right click in the intensity bar to the right of the image display see Figure 6 6 M oam 1 m Black On white 11 Colored CUSTOM DIFFER Life 1000 MONG Trichi PRINT List Fre ce oS Rainbow Rainbow Step The Blues Tie Dye 16 5 va VIDEO White On Black Custom Figure 6 6 Color tool After the
50. akage APEX2 User Manual The timing shutter is a device which pre cisely controls the exposure time for each frame during data collection Its status lamps indicate when the shutter is open ON and closed OFF For SMART APEX systems this assembly also houses an automatic attenuator Kappa APEX II sys tems do not have an attenuator The incident collimator is equipped with pin holes at both front near crystal and rear near source These pinholes help to define the size and shape of the incident X ray beam that strikes the specimen Collima tors are available in a variety of sizes depending on your application The beam stop catches the remainder of the direct beam after it has passed the speci men The beam stop has been aligned to minimize scattered X rays and to prevent the direct beam from hitting the detector The entire collimator assembly is supported by a collimator support assembly which has been precisely aligned to guarantee that the X ray beam passes through the center of the goniometer M86 E00078 APEX2 User Manual 2 1 3 Video Camera microscope heading The video camera an essential part of the sys tem allows you to visualize the crystal to opti cally align it in the X ray beam and to measure the crystal dimensions and index crystal faces The camera is interfaced to the computer and is operated through the VIDEO program The video program includes several computer gen erated reticules
51. all noise peaks removed 9 8 M86 E00078 APEX2 User Manual Structure Solution and Refinement 9 3 2 Label the Atoms 1 Label the atoms and set the atom types Left click on atoms to select them Left click on the peaks for the two oxygen atoms Q2 and Q5 in this example Figure 9 11 View of model with the probable oxygen peaks selected M86 E00078 9 9 Structure Solution and Refinement 2 If it is difficult to see the color and labels change the color scheme by left clicking on Preferences and then right clicking on Background Color Choose colors and click Apply Click Cancel to exit the background color mode Note that the selected peaks are blue in Figure 9 13 Preferences Help Atom Preferences OpenGL Preferences shel cur style Color Ctrl B SELECT BACKGROUND COLOR Solid f Gradient Foreground Background Apply Cancel Figure 9 12 Selecting the background color APEX2 User Manual M86 E00078 APEX2 User Manual Structure Solution and Refinement The Atom Labelling box will open ATOM LABELLING IN ORDER OF SELECTION Element El First Sequence Ascending Suffix Descending Relabel Cancel Figure 9 15 Atom Labelling box 4 The two selected atoms need to be changed to oxygen atoms Do this one of two ways e Click on the Element field and type in the element symbol case does not matter e Click on the El
52. are of interest add mpla cards M86 E00078 APEX2 User Manual 9 3 8 Generate an Atomic Displacement Thermal Ellipsoid Plot 1 Remove difference peaks with the slider tool 2 Right click on the background and select Thermal Ellipsoids Figure 9 49 Thermal ellipsoids with large hydrogen atoms 3 Ifthe hydrogen atoms in Figure 9 49 are large change their size 3 1 Click on preferences in the Window Tool Bar and choose Atom Prefer ences Preferences Help Atom Preferences Figure 9 50 Atom preferences tool M86 E00078 Structure Solution and Refinement At the top of the box that is opened there are three values that can be changed to change the size of atoms and the bonds to them PREFERENCES Element 4tom Radius Bond Radius PeriodicT able 12 22 Figure 9 51 Default atom preferences 4 Change the hydrogen radius to 0 08 and the bond radius to 0 15 to make the hydrogen atoms smaller 3 PREFERENCES Element 4tom Radius Bond Radius PeriodicT able 0 08 0 15 Figure 9 52 Modified atom preferences Figure 9 53 Thermal ellipsoid plot with smaller hydrogen atoms Structure Solution and Refinement 5 Position atom labels by right clicking on the atom and choosing Position Label Delete Atom Hide Atom Labelling Set Pivot Point Hide Label Position Lebel Change Part Figure 9 54 Position Label menu Figure 9
53. avail able for user customization or manipulation It must be running before the APEX2 Suite is started and it should be stopped before the computer is shutdown see Section 4 3 2 The purpose of the database is for storage of data generated by the Bruker APEX2 software APEX2 User Manual M86 E00078 APEX2 User Manual Software Overview 3 2 2 APEX2 GUI e Window Tool Bar The APEX2 GUI has one main window see Fig ure 3 5 This window is divided into four sec tions Tool Icon Bar e Task Bar e Task Display Area File Instrument Windows Window Tool Bar Tool Icon Bar Jo BN i Setup i nmm Describe Task Display Area Evaluate Crystal Solve Structure Refine Structure Figure 3 5 APEX2 GUI M86 E00078 Software Overview Window Tool Bar The tool bar provides pull down menus for a variety of file operations image tools and help files Option Description Symbol Use this menu to select the following Restore Move Size Minimize Maxi mize and Close File Use this menu to select the following Login Logout New Open Save Close Import Spatial Export P4P File and Exit Use this menu to select the following Connection Status Toggle Shutter and Abort Use this menu to select the following Cascade and Tile Instrument Windows RLATT Use this menu to select the following available when Rotate Edit Orientation Unit Cell Tool you select Mea
54. bridize All Calculate Hydrogens Figure 9 39 Refine028 APEX2 User Manual Figure 9 40 Model with added Hydrogen atoms 3 The following warning will appear indicating that the hydrogen atoms have been provi sionally added and that the final addition with naming will take place when the least squares calculations are started Click OK MSHELL has only assigned atom types Correct labels Will be generated during the next refinement cycle Figure 9 41 Hydrogen atom warning M86 E00078 APEX2 User Manual 4 Click on the Refine button to launch the least squares refinement program The out put window will open and a summary of the results of individual cycles of refinement will appear GooF S 0 482 Restrained Goof 0 482 for D restraints Mean shift esd 0 506 Maximum 2 502 for C11 at 11 53 17 Max shift 2 0 011 A for H11B Max dU 0 000 for C1 wR2 0 0781 before cycle 3for 2445 data and 129 129 parameters GooF S 0 475 Restrained Goof 0 475 for D restraints Mean shift esd 0 034 Maximum 0 243 for U13 C4 at 11 53 17 shift 0 001 for H11B Max dU 0 000 for C5 wR2 0 0781 before cycle 4 for 2445 data and 129 129 parameters GooF S 0475 Restrained Goof 0 475 for D restraints Mean shift esd 0 009 Maximum 0 070 for tors H114 at 11 53 17 shift 0 001 for H11B Max dU 0 000 for C5 wR2 0 0781 before cycle 5 for 2445 data and 2 129 parameters GooF
55. e 9 28 Refine2015 3 Right click on the background and click on Information on All Atoms Find Duplicate Labels Information on All Atoms Hydrogen atoms k Figure 9 29 refine 2005 M86 E00078 9 19 Structure Solution and Refinement APEX2 User Manual This produces the table in Figure 9 30 Information On All Atoms INFORMATION ON ALL ATOMS x v gt _ crane uo 0 8097 0 1815 0 0353467 0 3345 0 3026 0 04722 0 8432 0 890 0 0488033 0 3591 0 1141 0 03482 0 1496 0 502 0 0549167 0 6896 0 8 0 03449 0 4329 0 1949 0 0335967 0 5093 0 24 0 0371967 0 6354 0 1245 0 0332767 0 1756 0 1410 0 0462133 0 8345 0 3779 0 04692 0 2978 0 620 0 0566333 0 4862 0 891 0 0486733 0 6496 0 1778 0 0572667 Figure 9 30 List of parameters with Ueq to the right Examining the values here is difficult because the atoms are not in order 9 20 M86 E00078 APEX2 User Manual 9 3 5 Sort Atoms 1 Right click on the background and click on Sort to sort the atoms into a sensible order m Hydrogen Labels m Labels Grow Pack Figure 9 31 Choose the Sort option A box will appear to the right of the molecule display Since 51 O1 and O2 are in a reason able order only the carbon atoms need to be ordered
56. e Queue Active Image Queue Images zi Figure 7 15 The Image Queue tool The Image Queue sets the number of frames being used to determine profiles For crystals with high mosaic spread big wide reflections increasing the queue size can improve integra tion 5 Click on the button on the far right of the bottom row Start Integration This will start the integration and will open the SaintChart window for monitoring the integration 6 Examine the output Double click on any of the output entries for one additional tool the Is button at the far right of the top This will open the SAINT listing file for that inte gration run see Figure 7 16 E 161 manualwerk lid manual iz 15 Figure 7 16 Using the runs list Is tool M86 APEX2 User Manual Data Integration and Scaling 7 2 Monitor the Integration Run with SaintChart SaintChart is a powerful tool for monitoring the progress of the calculation and for graphically presenting the results of the integration process SaintChart Chart Windows saan Sepe SS Al Comporerts D Progett States C progress Perimoge Stories Spot shape cometahon Spee eternity ond 17 x5purisechy 2 O Number of seflections harvested Sra potters overlay O 29 5 Queue exteri used bem intensity Cd
57. e are often a few reflections that are not indexed The reciprocal lattice viewer can be used to look at the spots used in the indexing but first refine this cell 3 Click on OK to accept the indexing results Data Collection 6 2 4 Refine the Unit Cell There is not a correct order for the following steps Use this as a guideline with the main goal of creating a stable converged refinement 1 Click Refine in the Indexing Tools menu The refinement window will open ba Deviation Histograms 2 xi APEX2 User Manual bd Refine Unit Cell 2 Detector Corrections Distance mm 0 00 Constrain Distance Beam X mm E 44 Beam Y mm fo 36 Constrain Beam Center Pitch fo 34 Roll 65 Yaw fo og Constrain Pitch Roll Yaw Crystal Position X mm o 00 Y mm o 00 2 mm 0 00 Constrain Crystal Position Goniometer Angle Zeros Omega fo oo Chi Kappa fo 00 Constrain Angle Zeros Display Image matrix _01_0001 sfrm C Show Observed Spots Show Predicted Spots Fit Unit Cell More Tolerant Total Spots 259 i ae 5 929 Axis 8 981 C Axis 18 348 4 Spots Fit 93 Alpha 83 355 2 RMS XY mm 0 00 Beta 89 811 E Gamma 83 353 RMS Angle 0 00 Volume 976 9 3 NEUEN Symmetry Constraint Less Tolerant Triclinic Refine Bravais Transform Orientation Matrix Figure 6 13
58. e used to change the display frequency of the Integrated Spots images The default is shown every fifth image amp Integrated Spots 5 ni xj Scan 4 Integration x l AI Components xl Progress Statistics VD Integration progress Per Image Statistics Spot shape correlation El Spot intensity and 1 5 1 D Spot intensity lt 2 Siama l HD Number of reflections harvested El Spot position overlay CE X Y Z error X Y Z RMS difference D X Y Z spot size O Queue extent used Primary beam intensity D Periodic Statistics iE Profile snapshots PD axis ESD UD Basis ESD D C axis ESD Alpha angle ESD Beta angle ESD Gamma angle ESD Cell volume ESD L5 goodness of fit O LS Residuals O X Y Z crystal translation X Y beam center O Distance correction Pitch Roll Yaw correction iO Angle zeros Coverage Statistics rorrnnupo ro gp rro o dr prrnup oor priu AD Harvested reflections 1 10 100 1000 10000 100000 1000000 oO Completeness and redundancy Bijvoet pairs Description 1 Image type Phi Scan Image Start position Distance 35 00 2Theta 28 00 Omega 48 51 Phi 57 End position Distance 35 00 2Theta 28 00 Omega 48 51 Phi 58 C 4 b Image Header Figure 7 21 Full view of the Spot Position Overlay M86 E000787 Data Integration and Scaling Data Integration and Scaling
59. ed two important files YLID1M p4p containing the final unit cell parameters and other impor tant information on how the experiment was car ried out and YLID1M raw containing the actual intensity data M86 E00078 These files are all that is required to begin the structure solution and refinement process The various steps in solving and refining the struc ture are carried out using the programs of the SHELXTL package Structure Solution and Refinement 9 2 Solve the Structure The process of obtaining an initial model of the compound is started by clicking in the Task Bar on Solve Structure and then on Structure Solu tion 1 This will open the Structure Solution GUI Check that there is a reasonable formula in the formula window nstructions Listing Y Results TITL ylid reso75 in PZ 1 2 1 2 1 CELL 0 71073 5 9634 9 0449 18 3942 90 000 30 000 90 000 ZERR 4 00 0 0005 0 0010 0 0021 0 000 0 000 0 000 LATT 1 SYMM 0 5 Y 0 547 SYMM X 0 54Y 0 5 Z SYMM 0 54X 0 5 Y Z SFACCHOS UNIT 44 48 8 4 APEX2 User Manual 1 1 If you entered a correct formula in the display GUI then all is ready to start a normal direct method run 1 2 If the formula is incorrect change it in the formula window and press Return The input file will update Base viia 75 Formula C11H12025 m Statistics Reflections 12251 Unique 1429 Rejected 75 Observed 1363 Ri int 357 Observed 3
60. efully remove from its case the goniome ter head containing the YLID test crystal 5 Place the goniometer head onto its base on the phi drive aligning the head s key slot with the key pin in the base 6 Snugly screw the head s collar to the base so the head does not move Do not over tighten it M86 E00078 APEX2 User Manual 5 2 Center and Align the Sample To obtain accurate unit cell dimensions and to collect good quality data align the center of the sample with the center of the X ray beam and maintain the alignment for the entire experi ment Your video camera should be aligned so the crosshairs of the video camera coincide with the center of the goniometer and the center of the X ray beam see manual M86 Exx024 for instructions on aligning the microscope to the center of the instrument Although if the micro scope is not centered you can still align the sample the key here is that the crystal stay in the same place in the microscope in all orienta tions NOTE On SMART APEX systems adjust the height while in the mount position NOTE Use the thin end on the goniometer wrench to unlock the adjustment slides at the beginning of the centering process and to lock them at the end locking needs only a very slight touch The other end of the wrench is used to make adjustments NOTE If the image of the crystal is difficult to see illuminate the sample with a high intensity M86 E00078 Crystal Or
61. ent Computer Shutdown llle 4 6 AS DIOODINGAP E X2 298 hie d aei aC ox E Re Sad oi dod d a RM Mete opp cU 4 6 4 3 2 Stopping the Database 4 6 4 4 Server Computer Shutdown 0 0 eee ees 4 7 4 4 1 Stopping the APEX2 Server 4 7 74 2 BIS Reds eats eee acere idee aus ss 4 7 5 Crystal Ori ntallOl Sess 5 1 5 1 Mount the Goniometer Head on the Instrument 5 2 5 2 Center and Align the Sample 5 3 6 Dala CONCCHON 6 1 6 1 Start New Project and Describe the Sample 6 1 6 2 Determine the Unit Cell 0 0 eee eens 6 3 622 1 Collect Images aon terret top eoe ripa ion deo et atc og don ddan o d dier uadit eet 6 3 6 2 2 Harvest the lt 6 6 6 2 9 Index the Helle CHORDS 4 525 3 d n n Eee dca Soa eae Pc EO Re OR ea ed 6 9 6 2 4 Refine the Unit Cell s deed ogee od ERES EU RR LEG ER DERE EU ES 6 10 6 2 5 Determine the Bravais 6 12 6 3 Determine the Data Collection Strategy 6 13 6 4 Data Collection Run
62. er values for the terminal atoms meth yls and carbonyls e sensible numbers for the six member ring lower for C8 and C9 higher for C5 and C6 and in between for C4 and C7 M86 E00078 Structure Solution and Refinement 9 3 6 Add Hydrogen Atoms At this point refine the hydrogen atoms either by renaming them using the labelling tool as before and then including them in the refine ment or Include the hydrogen atoms in fixed idealized positions riding on the atom to which they are attached In this manual we will illustrate the later fixed idealized method NOTE In some cases e g hydrogen atoms on hetero atoms or on geometrically strained car bon atoms it is better to refine the hydrogen atom positions A general rule is to refine if there is some doubt about the position of the hydro gen atom and there is different electron density present Structure Solution and Refinement 1 Using the slider tool remove all of the hydrogen atoms Figure 9 37 Retread model with difference peaks removed 2 Right click in the background and the click on Hybridize All Add Hydrogen atoms TIR m Calculate Hydrogens Figure 9 38 Refine025 The colors of the atom labels will change to indi cate the atom hybridization NOTE If the atom hybridizations are hard to see right click on the background and open the Information on All Atoms window Lnrormaction on Aramis Add Hydrogen atoms Hy
63. eration Yes Append Strategy Append Matrix Strategy Validate Execute Sese Figure 6 23 Experiment view with strategy appended M86 E00078 6 19 Data Collection NOTE At the top of the experiment window are controls for data collection Usually the default values are correct For data collection times of less than five seconds correlation can usually be turned off If new dark frames are required APEX2 will automatically collect them Checking Generate New Darks will force the collection of darks before every run In Figure 6 23 the time and width are explicitly set for each run so changing the default width and time will have no affect If the explicit time or width for a run is deleted so the box is empty the default values will appear and be used 5 Click Execute Resume The focus will shift to Monitor Experiment and images will start to appear This may take a minute or two if new darks are being collected Images will start to appear NOTE When resuming after a power failure APEX2 will automatically skip images that were previously collected with matching angles and generator settings Otherwise it will ask if you want to overwrite the images NOTE After data collection is started the experiment window can be closed and APEX2 can be stopped The server computer must be left on If communications are lost between the 6 20 APEX2 User Manual client and the server frame data is stored on
64. first run is completed there usually is sufficient information to start the indexing step If state usually then need to give informa tion about what to do if there isn t enough information NOTE APEX2 assigns to every collected frame a name Per Ludger base name run frame sfrm APEX2 User Manual 6 2 2 Harvest the Reflections 1 Left click on Evaluate Crystal gt Determine Unit cell Determine Unit Cell m m Reciprocal Lattice Viewer Figure 6 7 The Determine Unit Cell Indexing icon M86 E00078 APEX2 User Manual This will open the image viewer but with a tool bar to the right for indexing See Figure 6 8 The plug in initializes with the first run e g matrix O1 First Image 01 0001 sim Number of Images 12 Clear All Reflections Harvest Spots Index Refine List Reflections i 0 Reflections Unit Cell A 10 000 4 e 90 000 B 10 000 4 90 000 C 10 000 4 30 000 Volume 1000 0 3 Symmetry Triclinic Lattice P E H Lar Lan Lan 1 100 1000 10000 100000 1000000 10 Description 1 Image type Phi Scan Image Start position Distance 40 00 2T heta 30 00 Omega 315 01 3 End position amp 40 00 2Theta 30 00 Omega 31 E k Detector Corrections Distance mm 0 00 Horizontal Beam Center mm 2 00
65. h to produce a series of diagnos tic plots Some of these are recaps of the plots that have already been displayed 2 Click on the folder tab at the bottom of the screen to select the individual plots as shown in Figure 7 27 Why To do what __ Statistics A Reflection Graphs A Refinement Graph A Error Model Graphs A Scale Variations Figure 7 27 Tabs for selecting diagnostic plots 7 20 M86 APEX2 User Manual The Scale Variations plot shows the overall vari ation in Scale and R int for the individual frames The Scale plot should be flat for highly absorbing irregularly shaped crystals it will probably be sinusoidal and the R int plot should not show large variations more than 2 Overall scale and int variations for ylid_manual Normalized Scale Factor Smoothed R 1int Run Frame gt M86 E000787 Data Integration and Scaling Data Integration and Scaling The Intensity Statistics plots look at R int and 2 1 as a function of resolution Typical plots of R int versus Resolution increase to the right as seen in Figure 7 29 An IE2 11 plot should have a constant resolution IE2 1l is a strong indicator of centric and acentric space groups The two horizontal lines indicate the expected values for centric top and acentric bottom space groups This plot clearly suggests an acentric space group fe M Pawose ienener Intensity statistics for manual R
66. he distance should be about the same as the longest cell dimension Typically distances ranging from 35 to 45 are reasonable 2 2 Set the exposure time and press return For normal crystals on an APEX Il five seconds is a reasonable time 2 3 Click Same to set all of the times to be the same NOTE If the Same feature is not chosen the times for shells can be set to collect high angle data more slowly than inner shell data 2 4 Set the desired redundancy 0 50 is a reasonable value APEX2 User Manual 2 5 Check the other values Laue class Lattice etc 2 6 Each time a value is changed COSMO recalculates the statistics for the runs The results are displayed in the column labeled Current 2 7 Below the Target and Priority columns is a pull down menu with several differ ent strategies Choose the one that best meets the needs of the experiment for the example Best in 2 hours cut this text we don t need to give a step by step analysis of the YLID At this point if all of the runs available were col lected it would take 183 98 hours and get a redundancy of 452 86 Clearly this is not desir able 3 Click on Refine Strategy 4 Alist of options will appear Again click Refine Strategy Execute Refine Strategy rateg y ES Sort RHursfer Completeness Figure 6 16 UserManual017 bmp NOTE The objective in refine strategy COSMO is to get good completion 9896 or
67. ientation lamp and or temporarily place a light colored piece of paper on the front of the detector NOTE Centering is often easier if the crystal is rotated to give a good view before the actual centering process is started e g down an edge for a plate To do this drive to one of the cen tering positions loosen the screw that locks the goniometer head rotate the crystal to a suitable orientation and then tighten the screw again 1 Click on the Center button the crystal and goniometer head will be positioned perpen dicular to the microscope To center the sample make adjustments in the height and with the translation screw that faces the front of the diffractometer Figure 5 2 Crystal initially mounted Crystal Orientation 2 Use the z axis translation screw and the x or y axis translation adjustment screw that is perpendicular to the microscope axis to move the crystal so it is centered in the microscope see Figure 5 8 and Figure 5 9 2 1 For the SMART APEX II Make adjust ments in the x and y translations but not to the height z Figure 5 3 Crystal centered 3 Adjust the height with the z axis screw 3 1 SMART APEX II Click on the Right button Adjust the height and the trans lation screw that is facing up 4 Adjust the translation with the x or y axis screw whichever is pointed toward you 5 Adjust the height again with the z axis screw 6 Adjust the crystal position usi
68. igure 8 10 Figure 8 13 or Figure 8 15 The default answer should new formula be E for exit Press Enter to accept this 2 2 n response to the question Enter For default mula type the correct formula C1 1 H12 O2 S1 and press Enter 2 3 Check that the information is correct Check that Z seems reasonable for the space group that the density is as expected 1 1 to 1 4 for organic mole cules higher for inorganic compounds and that the atomic volume is around 17 or 18 Significant variation from the expected values may indicate an incor rect molecular formula or missing counter ions or solvates The values at the bottom of the window look fine for the YLID Press Enter to accept 8 6 M86 E00078 APEX2 User Manual Examine Data E XPREP Ver 6 14 W95 98 NT 2000 ME Copyright Bruke 3 The next default action for XPREP is to write out the files necessary for the structure solution process see Figure 8 18 Press Enter to accept Current dataset Wave length Chiral Original cell Esds Current cell Matrix Crystal system space group E Formula Formula wt gt FE Density kE wo Lis 3 Mu rum 1 Figure 8 17 Defining and checking the unit cell contents Figure 8 18 Requesting output files M86 E00078 8 7 Examine Data 4 The program asks for an output file name Since this data has been cutoff at a resolu tion of 0 75A it makes sense to change the output file name to ylid_res75 to reflect the
69. iini blue Rsigma red Riint 2 1 for general hk Resolution df A Figure 7 29 Intensity Statistics APEX2 User Manual The plots Chi Squared values for the data as a function of resolution and intensity should be mosily flat Values below one are not unusual for weaker high resolution data The plots shown in Figure 7 30 are typical Chi squared distributions for ylid_manual Chi squared Mean of N Sum l lt L Li Sucen su iE CN equivalents 5 4 T al a L 2 1 1 5 L 0 9 0 5 0 7 Resolution d 5 Chi squared 0 1 0 2 0 3 0 4 0 5 0 6 0 7 0 8 0 9 Intensity quantiles Figure 7 30 Chi squared M86 APEX2 User Manual The special distribution plots are generated for each data collection run They indicate using red and blue dots points of average intensity for a particular reflection after scaling The actual intensity measured at that spot on the detector vary by more than three standard deviations Figure 7 31 show two spatial distribution plots side by side This is the way they are typically output by Scale Spatial distribution of L L Vsu for ylid_manual Spatial distribution of 1 L su tor vid_manual Sean L detector theta 72 23 isu blae emors black Sean 2 detector 2 theta 32 00 23 rede blue errors black Figure 7 31 Spatial distribution M86 E000787 Data
70. in a retrieval system transmitted or reproduced in any way including but not limited to photocopy photography magnetic or other record without prior written per mission of Bruker AXS Inc Address comments to Technical Publications Department Bruker AXS Inc 5465 East Cheryl Parkway Madison Wisconsin 53711 5373 USA All trademarks and registered trademarks are the sole property of their respective owners Printed in the U S A i M86 E00078 7 04 Table of Contents EC m i T ADIFOCGUC uou ob ae xoti E qua Gase wa ad eee econ eee 1 1 1 1 APEX II Systems for Chemical Crystallography 1 1 1 2 USerManvalFeawres 3224 2 1 9 epa eased hee d edo eat a eol ee eae 1 2 TO ray Sally ET 1 3 2 Hardware 2 1 2 l System oombpoLelils 231 9 5 59 29392 080 Modos vp pus Velia ee ed ed 2 1 21 0 APEXILDeIOCIOE Rod eu eee eee Erg ee dE dcn 2 3 2 1 2 GOnDIONmelef is sted oaa auus BER BE dd eu dicte td eta 2 3 2 1 3 Video Camera microscope 2 7 2 1 4 K780 X ray eee teen eee 2 7 2 1 5 Radiation Safety Enclosure with Interlocks and Warning Lights 2 7 2 1 0 DS GontrolleEu sa ed DE ETE xcd iE Eu E ER x di ad i eas aas 2 7 2 1 7 Refrigerated Recirculator for the Detector
71. inity unless safety precautions are completely understood and implemented All persons designated to operate or perform maintenance need to be fully trained on the nature of radiation X ray generating equipment and radiation safety All users of the X ray equipment are required to accurately monitor X ray exposure by proper use of X ray dosimeters For safety issues related to the operation and maintenance of your particular X ray generator diffractometer and shield enclosure please refer to the manufacturer operation manuals or your Radiation Protection Supervisor The user is responsible for compliance with local safety reg ulations M86 E00078 Introduction Introduction APEX2 User Manual 1 4 M86 E00078 2 Hardware Overview The two hardware platforms for the APEX II sys 2 1 System Components tems are the Kappa APEX 1 the four axis advanced research instrument and the SMART APEX Il the three axis laboratory instrument Software functionality is essentially the same for e APEX II CCD detector both platforms The system Figure 2 1 and Figure 2 2 consists of the following basic components e 4 Kappa or 3 axis goniometer e K780 X ray generator e Radiation safety enclosure with interlocks and warning lights e D8 controller e Refrigerated recirculator for the detector e Computer s two for the Kappa APEX II and one for the SMART APEX II e Video microscope e Accessories temperature devices
72. iting Figure 4 2 BIS warning message APEX2 User Manual NOTE With a SMART APEX II or a Kappa APEX Il the kappa goniometer will home and the kappa server will activate when BIS is started This may take a minute or two The server is a service tool and should not be used to control the instrument M86 E00078 APEX2 User Manual Program Start Up and Shutdown 4 1 2 Starting the APEX2 Server 2 Inthe top left corner click on the pull down 1 Click on Start gt Programs gt Bruker Nonius s Programs gt APEX2 Server Bg Apex2Server v1 0 19 A window will appear see Figure 4 3 File Instrument Windows b a Apex2Server 1 0 19 File Instrument Windows IL x Ik PEURA Toggle Shutter Center Crystal Simple Scans Center Crystal Figure 4 4 Connecting to the instrument 3 Click on Connection and a new window will appear see Figure 4 5 The name of your server should already be filled in 4 Click on connect a z la g Instrument Connection Hast Figure 4 3 Initial APEX Server window Cancel Figure 4 5 Connection window NOTE If the name is wrong then the instrument is not properly configured and you should con sult the system manager It is possible to con figure the instrument to automatically connect and then this window will not appear tell how to do this M86 E00078 4 3 Program Start Up and Shutdown 4
73. k on the arrow to the right of Direct 1 in the Method box see Figure 9 3 This gives three choices for structure solution using direct methods Method Structure Expansion Computing Effort scale Figure 9 3 Method box M86 E00078 Structure Solution and Refinement In most cases the default values will give a good initial model but there are several other options available for more difficult problems Chose the solution method by clicking the appropriate radio button on the left in the Method box Highlight and click on Direct 1 to set up a default run with a simple TREF instruction Highlight and click on Direct 2 to set up an extended run with TREF 10000 By adding 10000 to the TREF command more attempts are made to determine a solution This will take more time but if you see a good solution in the output window it is pos sible to stop at that point by clicking on the STOP button Good solutions typically have a CFOM of 0 06 or less Highlight and click on Direct 3 to set up an extreme run with two instructions ESEL 1 0 and TREF 100000 By adding ESEL 1 0 more reflections are used in the solution process This is particularly useful for acen tric triclinic structures and for pseudo sym metric structures Increasing the number of tries in the TREF command to 100000 runs until ended by clicking on the STOP button There is only one predefined option for the dual space calculations and also
74. lid manua Figure 7 8 Example of manually editing a run list 2 Check the refinement defaults The two buttons on the bottom far left are used to change the default options for the refinement of the data M86 E000787 Data Integration and Scaling The default values are generally very good There is seldom any need to change those in the refine window kr Retinement Optlons Perd races Flefnemert Enable Orientation Dancing Factor 1 005 Enable Sine yt Er Mefinemesnt Enable Global F Frequency maget 3 Max Humber ot Beecher inc Metric Sommeisy of Unit Cell bec of Ural eil Space Groups f Space finn P222 Crta Systeme Gees 1 Margin an esr enter Velia Beam Genta Distance Figure 7 9 Refine Window 3 Change the default options for the integra tion in the Integration Options window The integration window has a few values that are changed more frequently EEETTDEUIDOOCOINMMENNNNNN nx po Model r Background Update Enrabia LS Firing Blend Profiles All Detector Flegions Iieraiy Sigma Lower Lint lor Model Profle Update 10000 of Model Profle Mai
75. mera Hardware Overview Kappa APEX Il Goniometer The Kappa goniometer uses a horizontally ori ented Kappa goniometer with 2 theta omega kappa and phi drives and a motorized DX track for setting the detector distance It includes mounting points for the video camera and for optional attachments such as the optional low temperature attachment Timing Incident Beam Stop Shutter Beam Safety Collimator Goniometer Sealed X ray Shutter Head Tube APEX II Detector Monochromator Kappa Stage Kappa Goniometer Figure 2 3 Kappa 4 axis goniometer components With the kappa angle the crystal can be ori ented at chi from 92 to 92 This leaves the top of the instrument open for easy access APEX2 User Manual M86 E00078 APEX2 User Manual SMART APEX Goniometer The SMART APEX II system uses a horizontally oriented D8 goniometer base with 2 theta omega and phi drives dovetail tracks for the X ray source and detector and an additional mounting track for accessories such as the video camera and optional low temperature attachment The 3 axis system incorporates a fixed chi stage with chi angle of approximately 54 74 and a phi drive with 360 rotation which is so compact that it swings into the incident beam collimator allowing free rotation in omega All four axes 20 w and intersect Rotary Shutter and Attenuator Fixed Chi Goniometer Beam Collimator Safe
76. n or if the com systematic absences for all possible glide pound is known to be chiral enter that infor planes and screw axes see Figure 8 3 mation see Figure 8 6 Generally it is These are displayed across the middle of sufficient to press Enter to start the space the figure By examining the number of group determination reflections with I gt 3 sigma l the mean intensities and the mean int sigma which should all be very small for a systematic absence XPREP derives a suggested space group P2 1 2 1 2 1 Press Enter to accept Figure 8 6 Space group options M86 E00078 8 3 Examine Data 8 3 Reflection Statistics Figure 8 9 Systematic absences and a suggested space group 1 XPREP returns to the general menu seen previously see Figure 8 5 This time D is chosen to evaluate the dataset Press Enter to accept 2 here are multiple choices for data manipu lation see Figure 8 10 S chooses a dis play of statistics XPREP Ver 6 14 W95 98 NT 2000 ME Copyright Bruke Index Data Filename or Source of Data current dataset Figure 8 10 The data manipulation menu APEX2 User Manual 3 The data can be merged in several ways Choose the merge all equivalents including Friedel mates option A see Figure 8 11 Press Enter to accept E XPREP Ver 6 14 W95 98 NT 2000 ME Copyright Bruk Current dataset Figure 8 11 The merge data menu 4 A table of statistics appears
77. ng the x or y axis screw APEX2 User Manual 7 Click on Drive Phi 180 and adjust adjust what x y again Figure 5 4 Drive Phi 180 8 Check the other translation how which one Repeat steps 3 and 4 as necessary to keep the crystal in line with the microscope 9 Click on Drive Phi 90 Figure 5 5 Drive Phi 90 M86 E00078 APEX2 User Manual microscope 10 Adjust the crystal position using the goniom eter screws Why adjusting now what are we adjusting 11 Click on Drive Phi 180 and adjust again adjust what x y Repeat steps 3 11 as necessary until x is cen tered Then adjust the height using the following steps 1 Click the Left button and note the height The goniometer drives to place the fiber horizontal and to the left 2 Click the Right button and check that the crystal height stays in the same place in the microscope 2 a If the height is in the same place you are done M86 E00078 Crystal Orientation 2 b If the height is not in the same place adjust the height and repeat steps 1 and 2 Figure 5 6 Check the crystal height 3 Click the Top button Figure 5 7 The crystal is centered The crystal is now centered on the instrument All of the next steps except removing the crys tal from the diffractometer are performed with APEX on the client computer Crystal Orientation APEX2 User Manual YLID Crystal SEM P ounting 3 io Se
78. nt Describe Specify crystal size color shape etc Center Center Crystal Evaluate Crystal Determine Unit Cell Determine unit cell and Bravais lattice type Reciprocal Lattice Viewer 3D visualization a Of lattice projected in reciprocal space Table 3 3 Task bar options Software Overview Data Collection Strategy Simulated data collection and determination strategy Experiment Sequence editor for data col lection experiments Oriented Scans Measure different images with the crystal aligned along the axes Integrate Images Integration of different data Scale Scale intensities and perform absorption correction Table 3 3 Task bar options APEX2 User Manual XPREP Space Group Determination Run XPREP prep Precession Images Create synthesized precession images based on measured frames Solve Structure Structure solution Refine Structure K Run XCIF to generate a report Table 3 3 Task bar options M86 E00078 APEX2 User Manual Task Display Area The task display area is the main area for tasks user input and selected output This area dis plays images the reflections used in indexing and the observed and predicted diffraction pat terns It also displays the runs for data collection and solution and refinement For version 1 22 Eile Instrument Windows View
79. o main items Align Crystal and Simple Scans see Fig ure 3 4 Apres Server v1 63 Simple Seams a 9 00 OB i 1 i i 1000 Ira cn Dittence 40 OQ zT hes Dunes DU Phe Chis 1 DEL 21 bre Donee DEC Pree EO I LE A d Figure 3 4 Simple Scans window M86 E00078 emen 40 2 E 2Thets a reas a4 a Py ns Scan 200 Wie 2 Exposuee Tier Sacra 2 Mew dak image 3X Ph 05 wide 2 0 Dire Software Overview Software Overview 3 2 The Client Computer The client can be any computer which is on the same network as the server For SMART APEX systems it is usually the same computer as the server The main portion of the APEX2 suite the APEX2 client runs on the client computer The client is a GUI with multiple plug ins or mod ules for different aspects of an experiment The client includes a database which stores relevant data from each step in the experiment Details of the functions available in the GUI will be explained in more detail later in the manual 3 2 1 Database and Database Connection As currently configured the database is used internally by the APEX2 Suite and is not
80. only one for the heavy atom Patterson methods At the end of the direct methods runs the output display will look like the figure Good figures of Structure Solution and Refinement merit are near 1 0 for Sigma 1 and M abs and less than 0 06 for Ralpha and the CFOM Struc tures can be solved with figures of merit that deviate from these numbers but they may require more effort If all looks reasonable click OK in the output display and Exit in the solutions plug in The next step is structure refinement using XSHELL APEX2 User Manual 9 3 XSHELL 9 3 1 Refine the Structure The structure solution step produced statistics that indicate a solution had been found The real proof is in the initial model that is produced XSHELL provides the tools to view the model and determine if it makes chemical sense 1 Start XShell the molecular viewing and refinement plug in by clicking on Refine otructure in the Task Bar and then on the Structure Refinement icon 2 This will open a window to select files for XShell In usual operations the file name will be preselected If a different file is desired select Browse EZ ba Select Files For XShell 2 x RES file C struc quest ylid_manual work ylid_resa 5 res Figure 9 4 The Select Files tool M86 E00078 APEX2 User Manual Structure Solution and Refinement 3 Click on OK to open a molecular display window ee ee
81. options to change the image m Wireframe Ball And Stick Thermal Ellipsoid Pipes Select atoms Hide Part s Show all Atoms Disassociate amp toms Unit Cell Hydrogen Labels lt lt Labels Sort Grow Pack Trim zoom Out Toggle Pan nd Rotate Restore Deleted Atoms Find Duplicate Labels Information on All Atoms Add Hydrogen atoms gt Figure 9 6 XSHELL menu APEX2 User Manual M86 E00078 APEX2 User Manual The Information On All Atoms option shows a list of the peaks and their heights The drop in height between Q13 the last real peak and Q14 the first noise peak is typical of a correct solution formation On All Atoms Structure Solution and Refinement INFORMATION ON ALL ATOMS 51 w z mem ces uo 0 0000 5 0 8105 0 1820 0 2401 sp3 0 0 05 2 161 0300 Q 0 6925 0 10 0 1253 sp3 0 0 05 foz 158 7400 Q 0 3333 0 3057 0 1756 5 3 0 0 05 4 155 9800 Q 0 4332 0 1961 0 1488 sp3 o 0 05 5 los 141 7900 Q 0 5055 0 3 0 685 sp3 0 0 05 e 95 141 6800 Q 0 8344 0 898 0 1307 sp3 o 0 05 7 140 8200 Q 0 6372 0 1262 0 1726 sp3 0 0 05 o 140 6700 Q 0 3537 0 1161 0 834 sp3 0 0 05 9 las 127 0800 Q 0 1821 0 1416 0 360 sp3 0 0 05 10 fo 109 9200 9 0 8324 0 3761 0 2281 5 3 0 0 05 1 fowo 109 4100 0 0 1499 0 486 0
82. r 6 14 W95 98 NT 2000 Copyrig Figure 8 2 Lattice statistics 2 XPREP determines the reduced cell based on the lattice entered above Since the lat tice was primitive and the magnitudes of the cell dimensions were proper a lt b lt c the Original and reduced cells are the same see Figure 8 3 Press Enter to search for a higher symmetry cell APEX2 User Manual XPREP Ver 6 14 W95 98 NT 2000 ME Copyright Bruke Wave length Current dataset original cell Esds Current cell Matrix Figure 8 3 Reduced cell For the YLID there is no higher symmetry cell found The program has determined that the YLID crystal has an orthorhombic primitive lat tice See Figure 8 4 Press Enter to accept Figure 8 4 Higher symmetry cells M86 E00078 APEX2 User Manual Examine Data 3 The next logical step is to determine the 5 XPREP has chosen the crystal system O Space group XPREP suggests this see see Figure 8 7 Press Enter to accept Figure 8 5 Press Enter to determine the space group XPREP Ver 6 14 W95 98 NT 2000 ME Copyright Bruke Current dataset Wave length Figure 8 7 Choose the crystal system Original cell Esds m vo 6 has chosen the crystal lattice P see Figure 8 8 Press Enter to accept Crystal system Figure 8 8 Choose the lattice ND 7 XPREP evaluates the data and looks at the 4 Ifthe space group is know
83. reening APEX2 User Manual 3 2 M86 E00078 Appendix C RLATT 1 Use the Reciprocal Lattice tool to look at the reflections SUBLATUS D PE E IS AE Layer Mode DISABLED JEN M j NE ONE M Figure C 1 UserManual013 bmp M86 E00078 RLATT APEX2 User Manual M86 E00078 Index DPS HKL Kaercher Strategy ProScale SADABS SAINT M86 E00047 SMART Sparks indexing XM XPREP Curt l Il add to this list of keywords If there are any you specifically want added write them in Index PROTEUM User Manual M86 E00047
84. rest 3 xj Find Runs in Directory Je struc guest data_manual ylid_manual Image Base Mame vid manual Browse Cancel Figure 7 6 Find Runs tool view Both the Import Runs from Experiment and the Find Runs buttons will generate a list of runs as shown in Figure 7 7 Space Group P222 E Starting Image Filename 1 C Sstruc guestsdata manualsulid manual ylid manua structures data For manualslid manualswork ylid n struc guestsdata manualsulid manual ylid manua 153 structures data For manualslid manualwork ylid n C Sstruc guestsdata manualsulid manualylid manua structuressdata For manualsulid manualswork ylid n struc guestsdata manualsulid manual yylid manua structures data For manualsulid manualswork ylid n E Figure 7 7 Completed runs list Figure 7 7 shows a run list entry being changed The original run is shown first and then the run with the starting image number modified In the last strip the number of frames to process has been changed APEX2 User Manual M86 APEX2 User Manual Double click on any of the fields in this list to open up that value for editing Sstrucsqguest data manualsvlid rianualsulid manua manual vlid_manualtylid manual O4 DO001 sfrmd G strucsquestdata manualsulid manualvlid manua D manualsulid manualylid manual 0051 struc squestdabta manualslid manualsulid manua gt slrucsquestsdata manualsulid manualsy
85. rt Up and Shutdown APEX2 User Manual 4 3 Client Computer Shutdown A window will appear and quickly disappear and the Start Database window will close Start Database NOTE The order of stopping these programs is gt checkpoint record is at 073275080 redo record is at 073275080 undo record is at 8 8 shutdown TRUE ion id 21669 next oid 83168 important If you attempt to close the database before APEX2 is stopped the database will remain open until APEX2 is stopped on reset by peer 4 3 1 Stopping APEX2 1 For Windows or Linux systems click on the Figure 4 12 Stop database screen X in the upper right corner of the window or click on File gt Exit in the upper left It is not NOTE Occasionally the windows won t disap necessary to disconnect from the instru pear and the Start Database window will display ment a smart shutdown request see Figure 4 12 This message means that the database is wait Taa StOpPPING INE Datapase ing to close until applications that it might write 1a For Windows systems click on Start gt Pro to are closed Exit APEX2 to solve this problem grams gt Bruker Nonius Programs gt Stop If the message still appears check for other pro Database or click on the Stop Database cesses that may still be running e g COSMO icon onum EY 1b For Linux systems in a terminal window enter bnrun stopdb or click on the Stop Database icon 4 6 M86 E00078 APEX
86. s File Name iid manudmeps 7 Title of Diagnostic Plots yid mana Log File maudmabs Use only centrosymmetric point groups Point Group mmm m Additional Spherical Absorption Correction of Equivilant Sphere Lambda 2 Correction Correction Factor fo 0015 Allow for crystal decomposition sz by B value refinement Extra Linear Correction to be Applied ies to Each Reflection EE Figure 7 24 FIG7 28a M86 E000787 Data Integration and Scaling 2 Click Next and check that the defaults are correct Generally the Absorber Type is all that changes Data Integration and Scaling 7 3 2 Parameter Refinement 1 Click on Refine Figure 7 25 shows a typical refinement result The R values are reduced and the Mean weight increases Typical final values are 3 4 for the R values and 0 95 0 98 for the Mean Weight File Instrument Windows By ax JB c E Setup Evaluate Crystal Mean l sigma Examine Data Solve Structure Alincid Refine Structure Instrument Figure 7 25 Xscale window after refinement Mean Weight 0 98 0 9798 0 9796 8 3 0 9794 0 9792 amp 0979 Direction Cosines Mean error 000 Maximum error fo 001 Data Statistics Maximum 2 8 fes 89 Wavelength 71074 Reflections 8331 Unique 2728 Data per frame p 59 Input of Data Mean o l threshold
87. sing as usual with the view plugin Figure 8 25 The progress bar NOTE This is a relatively slow calculation since every sfrm file is examined to determine if it has pixels that would contribute to a requested zone For example if the Okl zone is requested with a thickness of 0 1 then the simulation is looking for all pixels to have 0 1 h 0 1 and any value including fractional values for k and l 5 Userthe simulated patterns to check space group symmetry see Figure 8 25 Figure 8 26 and Figure 8 27 and to find signs of twinning see Figure 8 28 having trouble generating acceptable images for 8 26 to 8 29 but they will get done eventually Include SIMPREC5 bmp here Figure 8 26 The plane for the test YLID Include SIMPREC6 bmp here Figure 8 27 The plane for the test Include SIMPREC7 bmp here Figure 8 28 The hkO plane for the test YLID Include SIMPREC7 bmp here Figure 8 29 A plane from a rotationally twinned crystal showing the two lattices Curt will add images of a good and bad exam ple M86 E00078 9 Structure Solution and Refinement 9 1 Overview You are now ready to solve and refine the crys tal structure for the YLID test crystal The vari ous steps in solving and refining the structure are carried out within the APEX2 GUI These tools will prepare input files for the solution and refinement programs of the SHELXTL package The integration process SAINT has produc
88. sure Distance Measure Angle and Reciprocal Visualization Lattice Viewer View Use this menu to select the following available when Detailed Strategy you select Data Collection Strategy Table 3 1 Window tool bar options APEX2 User Manual Tool Icon Bar The tool icon bar provides shortcuts to the options available through the window tool bar icon Description Create a new file e Open a file a Save a file What s this context sensitive help Open an image zl Select previous image This icon is visible a only when an image is open Select next image This icon is visible only gt when image is open Draw a circle This icon is visible only when Co an image is open Table 3 2 Tool icon bar options M86 E00078 APEX2 User Manual icon Description Draw a plotting line This icon is visible only A when an image is open Change the part of the image displayed while ae zoomed in This icon is visible only when an image is open Select a region of the image This icon is visi E ble only when an image is open Table 3 2 Tool icon bar options M86 E00078 Software Overview Task Bar The task bar provides menus for all of the options in the APEX2 Suite crystal evaluation and indexing Evaluate Crystal data collection Collect data processing Integrate and Scale and instrument setup Instrume
89. t storage of raw frame data integration of the data and solution and refinement of the struc ture Often the computer s is are attached to a net work of similarly configured computers with access to local and or network printers NOTE Connection to the external network must be done with care Consult with local security experts APEX2 User Manual 2 1 9 Accessories Various devices can be mounted on the goniom eter base These include optional low and high temperature attachments Both instruments can be used with diamond anvil cells M86 E00078 3 Software Overview This section presents an outline of the system server and the client execute on the same com software including a brief description of the soft puter but the functionality remains separate ware layout as well as the graphical user inter The flowchart in Figure 3 1 shows the software face GUI layout For both Kappa APEX II and SMART APEX II systems the server and client commu APEX2 runs on two computers the server and nicate using TCP IP protocol the client For SMART APEX II systems the APEX Suite Server TCP IP Connection Client Hardware Control BIS Data Collection Crystal Orientation and Evaluation APEX2 Server APEX2 GUI Figure 3 1 APEX2 software diagram M86 E00078 3 Software Overview APEX2 User Manual 3 1 The Server Computer The server computer communicates with the hardware allowing the user to con
90. ted weights vary signifi cantly from 0 06 and 0 00 then change the val ues to 0 06 and 0 00 Number of residual Q peaks ___ Figure 9 44 Refine032 Structure Solution and Refinement Late stage refinement options Refine all non H atoms anisotropically Use suggested weights Squared Term 058500 Linear Term o 000000 Refine extinction parameter Generate ACTA CIF information file Refine Edit File Cancel Figure 9 45 Select weights and request ACTA output 2 Click on Edit File choose INS and click OK to open the instruction file for the XL This allows you to add instructions that are not directly available in the GUI Open File For Editing vlid reso67 Squared Term Linear Term foc ine extinction parame erate ACTA CIF infe Cancel Figure 9 46 Open the ins file for editing 3 Check that the temperature card is correct 3 1 If torsion angles are of interest add a CONF confirmation TEMP 23 conf mola 12 cl c2 c3 c4 c5 c cH 51 01 of cl cll mola 6 c4 c5 c cB cl 01 of 51 c10 c11 mola 5 c8 c9 cl c3 cd c5 c 01 of 51 cll mola 10 cl c2 c4 c5 c cH 51 ol of clo cll Figure 9 47 Add instructions in the ins file APEX2 User Manual Figure 9 48 Difference peaks 4 Display the anisotropic atoms displacement parameters for the YLID If planarity and angles between planes
91. the Server Sean Sun penton 3500 2Thetae 308 Deepen 286 598 Ch183 Diane 350 2 E 99 Phi 1 11 343 Sean pmm Figure 6 24 Monitor experiment view M86 E00078 7 Data Integration and Scaling Before the data can be used to solve and refine the crystal structure convert the information recorded on the frames to a set of integrated intensities and scale all of the data M86 E000787 1 Data Integration and Scaling 7 1 Integration 1 Click on Integrate in the Task Bar 2 Click on the Integrate Images icon The fol lowing window will open Resolution Limit A 0551 Space Group Starting Image Filename g Output Filename t t Ei Refinement Options Integration Options Find Runs Import Runs from Experiment Start Integration Figure 7 1 Initial integration window 3 Check the default values There are two items of interest on the top of the window The space group tool and the resolu tion limit value Space Group 222 k i Figure 7 2 The space group tool APEX2 User Manual M86 APEX2 User Manual The space group tool allows the user to set the symmetry for integration Typically this value is correct when the integration window opens Group P222 Gtartin Triclinic Monoclinic
92. toff of infinity Figure 8 14 The resolution cutoff menu 2 Applying the cutoff removes approximately 3000 reflections from the data set see Fig ure 8 15 The next step is to see if the cut off has improved the statistics Type S and press Enter XPREP Ver 6 14 W95 98 NT 2000 ME Copyright Bruke Data Index Filename or Source of Data lt current dataset Figure 8 15 Requesting statistics after applying a high resolution cutoff 3 As before in step 3 enter A to merge all equivalents Examine Data APEX2 User Manual 4 After the cutoff all of the statistics look bet 8 5 Preparing an Output File ter See Figure 8 16 Press Enter to con tinue 1 Exit the data manipulation menu to return to the general menu This time chose C to define the unit cell contents Resolution Data Theory Complete Redundancy Mean I Mean I s Rint Rsigma 2 A window will open displaying the current formula Z the density and the atomic vol ume see Figure 8 17 In this example the formula is incorrect and Z has been set to six to try to achieve a reasonable density and atomic volume Since this formula is incorrect it must be modified now The cor rect chemical formula for the YLID crystal is C11 H10 O2 S 2 1 At Select Option do not accept the default answer of E Type in F to enter a Figure 8 16 Statistics after high resolution cutoff 5 This response will return to the data manip ulation menu see F
93. tool view Cancel Figure A 4 Find Matrix tool view 7 This defines the information on the runs but the defaults for space group and resolution have not been updated Click on space group and select the correct space group in this case Pmmm M86 E00078 APEX2 User Manual SAINTPLUS this case Generate Active Mask has been turned on and set to 0 7 1 Active 2 1 Generate Mask Triclinic Monoclinic 01 0002 gor Fractional Lower Limit of Average Intensity 0 700 ela Dor 1 Use Pre Existing Mask Rhombohedral i Prca i amp ctive kask File amy ns Hexagonal C Pmn2 1 Cubic Phaz Figure A 6 Active Mask tool Integration Option 2 1 9 BUE 10 Click on Start Integration to start the calcu lations and open the SaintChart window for monitoring the results Figure A 5 Space group tool 8 Double click on the Resolution Limit and enter an appropriate value NOTE If the starting values for SAINT need to be changed frequently change the default by modifying the SAINT ini file Consult the SAINT manual 269 01 75xx for further information on Windows or Linux 9 Usethe Refinement Options and Integration Options buttons to set up the Saint run In M86 E00078 SAINTPLUS APEX2 User Manual M86 E00078 Appendix B Crystal Screening crystal selection and mounting M86 E00078 Crystal Sc
94. trol the instru ment The software to align the system as well as to align and screen samples runs on the server computer 3 1 1 Bruker Instrument Service BIS BIS provides the link between the hardware and software Once a connection is established BIS executes hardware commands sent by the APEX2 software The instrument service can also be used as a service tool displaying diag nostic messages during operation Figure 3 2 Image of start stop in BIS 3 1 2 Bruker Control Program BCP BCP is used to configure BIS as well as to pro vide instrument control and alignment tools S BrukerInstrument ini BCP Bruker Configuratio File Edit View Tools Help c 1 DSTOOLS Generator Ctrl ShFt G Detector Bias Gtrl Shrt 6 Ratemeter Ctrl ShFt R Half beam Ctrl ShFt k TA HI STAR grid Ctrl Shft H Test Frame Ctrl ShFt T Configuration Dark Current Ctrl 5hft D Bad Pixels Ctrl ShFt P 3 Spatial Ctrl ShFt S Tiris Flood Field Ctrl ShFt F Attenuator Gerl Shrt 4 Imagemeter Ctrl ShFt I a Robot amp Dewars Manual Ctrl ShFt M Limits Ctrii Shft L Collision recovery Ctrl Shft C Update amp home Ctrl Shft U Encoder Offsets Ctrl Shft E Loa Test Security Exercise test Debug BIS Figure 3 3 BCP main window M86 E00078 APEX2 User Manual 3 1 3 APEX2 Server The APEX2 Server provides tools for aligning and screening samples There are tw
95. ty Stage Head y Shutter APEX Sealed X ray Detector Tube Monochromator Goniometer Figure 2 4 SMART goniometer components M86 E00078 Hardware Overview Hardware Overview X ray Source Three components comprise the X ray source a shielded X ray tube an X ray safety shutter and a graphite crystal monochromator The sealed tube X ray source with a molybde num Mo target produces the X ray beam used by the system The X ray safety shutter is built into the X ray tube shield The shutter opens upon initiation of a set of exposures and closes upon the end of collection Status lamps on the shutter housing indicate when the shutter is open red and closed green The shutter is also interfaced to the controller and to the safety interlocks A tunable graphite crystal monochromator selects only the K line A 0 71073 A emitted from the Mo X ray source and passes it down the collimator system Timing Shutter and Collimator On SMART APEX II systems the monochro matic X ray beam then passes through the laby rinth the timing shutter and the incident beam collimator before striking the specimen On Kappa APEX II systems the monochromatic X rays pass through a small labyrinth the timing shutter a secondary labyrinth and the incident beam collimator before striking the sample e The labyrinth is a device that ensures that the collimator and shutter are tightly con nected to prevent X ray le
96. um foe Single Sum Mad niena ipee Lind ler LS Mode Protea 0000 Lower Merokon Limi foe LS Model Profle on Mose phon Pofexvzhaewiehe a a Background Update Sealing Factor 1 000 j image usus Acher Image sue Hal wath fmages 7 E Bea Mondo H ca cmm Figure 7 10 Integration Options Data Integration and Scaling The default values in the Model Profiles window are usually good Model Profiles Blend Profiles from All Detector Regions Intensity Sigma Lower Limit for Model Profile Update 10 000 Fraction of Model Profile Maximum for Simple Sum Mask 0 050 Intensity Sigma Upper Limit for LS Model Profile Fit 9 000 Lower Resolution Limit for L5 Model Profile Fit 9999 000 Profile XYZ 4 4 4 Figure 7 11 Model Profiles For weakly diffracting crystals it is sometimes helpful to change some options in the Model Profiles window Reducing the Intensity Sigma ratios from 10 and 9 to for example 5 and 4 or 3 gives the profile fitting algorithm more reflec tions to model Clicking on Blend Profiles from All Detector Regions to increase the profile blending can also help with weakly diffracting crystals 4 Click on More Options This results in an expanded window see Figure and gives access to several other useful features in particular Active Mask see Fig
97. ure 7 13 Algorithm see Figure 7 14 and Image Queue see Figure 7 15 APEX2 User Manual M86 APEX2 User Manual Data Integration and Scaling Integration Options z Active Mask File am y Figure 7 12 The Integration Options window with More Options selected M86 E000787 APEX2 User Manual Data Integration and Scaling 7 1 1 Active Mask Active Mask Generate Mask Fractional Lower Limit of Average Intensity 0 000 Use Pre Existing Mask Active Mask File am ns Figure 7 13 The Active Mask tool The Active Mask is used to mask out areas that are covered by the beam stop low temp nozzle or other obstructions Typically a value of 0 7 is good here SAINT will determine an active mask for each run NOTE If this option is set the user should examine the active mask images that are written into the work directory These images can be opened with the image viewer They should be all red except for a black area showing the shape of the obstruction typically the beam Stop 7 1 2 Algorithm Algonthm C Use Narrow Frame Algorithm f Use Wide Frame Algorithm Figure 7 14 The narrow wide algorithm tool The algorithm buttons are used to change from narrow to wide frame integration Frames col lected with narrow scans width less than one should be integrated as narrow frames Those greater than one should be integrated as wide frames 7 1 3 Image Queue mag
98. utdown As mentioned previously the APEX2 Suite is composed of several programs All of the pro grams are started in a similar fashion For ease of use there is usually a desktop icon for the folder containing these programs and desktop icons directly to these programs However the Click on Start gt Programs gt Bruker path is always available This more complicated method is what will be used in this discussion M86 E00078 4 1 Server Computer Start Up Two programs must be running Bruker Instru ment Service and APEX2 Server NOTE For Kappa APEX II systems the pro grams will be on the server computer in the goniometer cabinet For SMART APEX Il sys tems there is typically only one computer 4 1 1 Starting Bruker Instrument Service BIS 1 Click on Start Programs Bruker AXS Programs Bruker Instrument Service After a brief initialization period a window will appear see Figure 4 1 On Kappa APEX II sys Program Start Up and Shutdown tems the goniometer will move to reference positions 00 Fie e e E w Figure 4 1 The BIS window If a small pop up window appears that says This second instance of BIS is exiting see Fig ure 4 2 BIS was already running Click on ok to clear this informational message InstrumentService AN This second instance of BIS is ex
99. ution Cutoff llle 8 5 8 5 Preparing an Quitput Files css E Aat PRCA 8 6 8 2 Simulated Precession Images 8 9 9 Structure Solution and Refinement 9 1 O 1 OWVerVIOM id ded s o dulcem ERR RC CA ACA Roe Gelb etn o oe C oed 9 1 The SU o en Qt CRAT a Ep eR doa Gace ane dos M xt P REC el 9 2 Ace CnJlzaMC r T 9 4 9 3 1 Refine the Structure llllleeeeeeeeeel ehh 9 4 9 9 2 ALIS ax aco poros rg deti e ORE E Bok oe eet a ae Ace 9 9 9 3 3 Refine the Molecule 9 14 9 3 4 Look at Atomic Displacement Parameters Thermal Ellipsoids 9 19 9 35 SOMAS DAE dot at E eee 9 21 M86 E00078 3 Table of Contents APEX2 User Manual 953 6 Add PydtegellATOITIS ead com ob Or an doe kal Kwai ge 9 23 9 3 7 Final Refinement for Publication 9 25 9 3 8 Generate an Atomic Displacement Thermal Ellipsoid Plot 9 27 Appendix A SAINTPLUS tance ee ieee tee A 1 Appendix B Crystal Screening B 1 Appendix 1 Add Twinabs Cell Now Index 4 M86 E00078 1
100. ws enter the command bnrun c Wn sre plugins Nsaintisaintplus pyc M86 E00078 see Figure A 1 For Linux enter the com mand bnrun usr local bn src plugins saint saintplus pyc Command Prompt bnrun c bn src plugins saint saintplus pyc struc guest ephe lt gt cd N ocd struc guest ephe 1t struc guest ephe 1t gt bnrun c bn sre plugins saint saintplus pyc Figure A 1 Starting SAINTPLUS SAINTPLUS After the command is executed the SaintPlus window will open see Figure A 2 ni xi File Options Utilities Space Group P1 Y Starting Image Filename 1 Images Matris Filename Output Filename APEX2 User Manual Resolution Limit fi 700 EMI 4 Zj 5 6 7 o Refinement Options Integration Options Find Runs Replace Matrix Files Figure A 2 Initial integration window This window is like the Saint window discussed previously but with the following differences e Defaults are not determined by previous knowledge of the sample Start Integration 6 Click on Replace Matrix Files and browse to find a p4p or spin file to use Replace Matrix Files New Matrix FR e There is a button to replace the matrix files 4 Click Find Runs Browse to find the images to integrate rx Find Runs in Directory Image Base Mame Cancel Figure A 3 Find Runs
101. ystem interruption device that senses when the doors and panels are open and prevents use of the shutter and data collection until you close the doors 2 1 6 D8 Controller The D8 controller is an electronic module enclosed in the rack behind the font panel of the instrument It contains all of the electronics and firmware for controlling the generator opening the X ray shutters and monitoring other instru ment functions such as safety interlocks gener ator status and detector statuses For SMART APEX II systems the goniometer is controlled by the D8 For Kappa APEX II systems there is an additional module the Kappa controller for positioning the Kappa goniometer angles and driving the detector distance Hardware Overview 2 1 7 Refrigerated Recirculator for the Detector The refrigerated recirculator uses an ethylene glycol water mixture to absorb the heat from dual Peltier devices which are used to cool the CCD chip to approximately 58 F 50 C This minimizes dark current 2 1 8 Computers The Kappa APEX system uses two high speed computers The server controls the instrument and is used for crystal centering and screening The client collects the data stores the raw frames processes the data and solves and refines the structure The two computers are linked via a hub and communicate with each other via TCP IP protocols The SMART APEX II system uses a single high speed computer for control of the experimen

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