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USER`S MANUAL

1. Manual Control Module Frame Buffer computer Radiation Safety Enclosure SMART APEX Pd Detector d ye AH _ m 2 AT Controller 4 ae 5 Generator ER Electronics Figure 3 1 SMART APEX system components M86 E04015 1001 3 1 Hardware Overview 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 incorporates interlocks for both hardware and software an automatic system 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 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 electro
2. nnn nns 4 3 4 3 Optically Align the Sample ssssssssssssessseeneeen nennen nnn nna nnn nns 4 7 4 4 Unit Cell Determination eeeesee Im IRR RR Rhet tremere retener 4 12 4 5 Data Collector csset rir rr Erba Rr rey e Yard ke Eae ye aen te 4 14 46 Least Squares Refinement essessssssesssssssssseeese eene nnne nn nsn sa nnn nenas 4 15 5 ee 5 1 6 Structure Determination amp REFINEMENT c cecececencecececeneecececenencececenencececenenceceaeneneeneaeaeaes 6 1 M86 E04015 1001 Table of Contents SMART APEX User s Manual i M86 E04015 1001 1 Introduction 1 1 SMART APEX Features The Bruker AXS SMART APEX system is the newest member the SMART CCD product line of instrumentation for single crystal X ray diffraction This system is completely redesigned and features a new CCD detector based upon a 4K CCD chip It also incorporates a new goniometer with an enhanced interface all enclosed in a fail safe X ray enclosure system From a software and operational viewpoint the SMART APEX system shares many common features with its predecessors SMART 1K SMART 2K SMART 1000 SMART 2000 SMART 1500 SMART 6000 and SMART 6500 These features are discussed in the SMART Reference Manual Al
3. BRUKER ADVANCED X RAY SOLUTIONS USER S MANUAL M86 E04015 1001 SMART APEX User s Manual This manual covers the SMART APEX software package To order additional copies of this publication request the part number shown at the bottom of this page 2001 Bruker AXS Inc All world rights reserved Printed in U S A Notice The information in this publication is provided for reference only All information contained in this publication 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 2001 Bruker AXS Inc Madison Wisconsin 53711 USA all world rights reserved Printed in the United States of America No part of this publication m
4. Lattice Wavelength 0 71073 Chiral 90 00 90 00 Vol 90 00 90 00 0 0000 0000 0000 1 0000 Define unit cell CONTENTS Set up shelxtl FILES RECIPROCAL space display UNIT CELL transformation Change TOLERANCES QUIT program SMART APEX User s Manual M86 E04015 1001 SMART APEX User s Manual Structure Determination amp Refinement 8 Press RETURN to choose the SPACE GROUP option S SMART will then prompt you for four selections determine space group S the crystal system O the lattice centering P and the space group A P21212 All prompts and data are shown in Figure 6 9 BIGXPREP V5 1 Copyright c 1997 Bruker AXS 5 Determine SPACE GROUP C Must be CHIRAL sample is N NOT NECESSARILY chiral may be racemate I INPUT knovn space group E EXIT to main menu or 0 QUIT program 4 Triclinic M Monoclinic 0 Orthorhomnbic T Tetragonal H Trigonal Hexadgonal C Cubic or E EXIT Lattice exceptions N total N int gt 3sigma Mean intensity Mean int sicgma Lattice type P A 9 O obv rhomb on hex Mean E E 1 968 centrosym and 736 non centrosyrm c absence exceptions a b n 11 127 121 122 E 100 100 94 5 214 1 244 4 195 3 6 22 9 45 5 21 7 5 6 145 6 Option Space Group Ho Tvpe Axes CS Rfint Nfeq Syst Abs P2 1 2 1 2 1 19 chiral 91 0 032 5070 Figure 6 9 Next XPREP window M86 E04015 1001
5. Locate a p p or data file to associate with the new project Look in Adi gx e aal YLID11 raw an YLID12 raw a YLID13 raw 3 YLID1m p4p in Files of type 4 hkl and raw files Cancel Project path D frames ylict SYLID1m Figure 6 3 Locate the YLID1m pd4p file The SHELXTL Program and Project Manager window appears Figure 6 4 C Shelxtl Program and Project Manager Project 5 XSHELL XL XP xwAT XPRO XCIF xFO0G XPOW XPS Edit Help Project name YLID1m Project path D frames ylid1 YLID1 Figure 6 4 SHELXTL Program and Project Manager window M86 E04015 1001 SMART APEX User s Manual Structure Determination amp Refinement 4 Click XPREP XPREP or XPREP BigXPREP The first XPREP window appears Figure 6 5 BIGXPREP V5 1 Copyright c 1997 Bruker AXS XPREP DATA PREPARATION amp RECIPROCAL SPACE EXPLORATION Ver 5 1 NT COPYRIGHT c 1997 Bruker Analytical X ray Systems 411 Rights Reserved T embed enndem pem Data multiplied by 0 1000 to bring onto reasonable scale o Reflections r I sigma Lattice exceptions total N int gt 3sigma Mean intensity e Mean int sicma Lattice type P J oby R rev rhormb on option Figure 6 5 First XPREP window M86 E04015 1001 6 3 Structure Determinati
6. TE HE HE HE HE HE HE HE HE HE HE HE HE HE HE HE HE HE HE dE E HE HE HE HE HE HE HE HE HE HE HE HE HE HE HE E dE HE dE dE HE HE HE HE HE HE HE HE HE HE HE HE dE dE dE dE dE E dE EE dE dE JE EHE ttt ttt ttt Y YLIDim finished at 16 47 10 Total elapsed time 1 9 secs THEE EEE EEE EEE EEE EEE EE EEE EEE EEE tt ttt ttt Print Figure 6 28 Least squares refinement In the output above note that the R1 value is 9 0 This is typical for a preliminary isotropic refinement with no H atoms included Also note that for our sample the program informs us that we must invert the molecule to obtain the correct absolute structure 6 20 M86 E04015 1001 SMART APEX User s Manual 32 Click OK to return to XSHELL The Q peaks on the diagram represent difference peaks 33 You may delete them with the Edit gt Kill all Q peaks command Figure 6 29 ylid1 m res olx File 8 79 Refine Select Atoms View Preferences Labels Render Help Edit Current File Kill all G Peaks Restore Killed amp tom s v EMOL after significant structure changes Figure 6 29 Kill all Q Peaks M86 E04015 1001 Structure Determination amp Refinement 34 Click the Refine button at the top of the XSHELL Menu A panel will appear Figure 6 30 Refinement Control Ea Cycles 4 Extinction 0011 Plan 5 zl Omit Anisolv Invet v Fourer Difference Map vom TUER Actal List None Weights Previous M
7. the X ray tube is aligned and that all software has been properly installed M86 E04015 1001 2 Software Overview The essential software components of the SMART APEX system located in the Bruker AXS program folder on your Windows NT desktop are SMART program SMART SMART program NE SMART off line VIDEO program videa M86 E04015 1001 This on line program controls the instrument to collect the experimental data used by the other programs in the system program suite This off line version performs many data display and manipulation functions but cannot control the instrument This program controls the real time video images from the video camera SAINT program SAINT 4 SHELXTL programs m SHELATL This program sets up and carries out the integration process This program suite produces a crystal structure from the integrated data 2 1 Software Overview SMART APEX User s Manual 2 2 M86 E04015 1001 3 Hardware Overview 3 1 SMART APEX System Components The SMART APEX system Figure 3 1 consists of the following basic components e 3 goniometer module with SMART APEX detector see Section 3 2 Radiation safety enclosure with interlocks and warning lights D8 controller Refrigerated recirculator for SMART APEX detector Computer 3 axis Goniometer Module with SMART APEX Detector
8. Background output frequency Corrections intensity esd s 0 000000 f 000000 Frames stored to monitor reflection overlap Active frame queue half width fz Crystal a o00000 Crystal f Instrument error fraction of intensity Factor multiplying intensity exd s Starting exposure time hours Batch Data Integration SMART APEX User s Manual 10 Click the Integrate Sort Global button to execute the SAINT program The integration process takes about 15 minutes displaying data as shown Figure 5 8 15 C SAXIASAINT32 SAINT exe olx rystal system constraint 5 Orthorhombi c Parameter constraint mask Eulerian angles 20 741 130 307 104 460 etector corrections X Cen Dist Pitch Roll Yaw 0 092 0 148 0 007 0 208 0 233 0 149 Refinement statistics StartingRes FinalRes GOF Cycles Code 8 0 2 03041E 02 1 65274E 02 0 81 Integration 03 06 00 08 12 06 Unsorted reflections will be written to D frames ylidl work unsorted raw Spatially corrected beam center 261 15 250 77 No reference intensity correction will be made Input monochromator 2Th roll deg 12 17 0 00 Input X Y Z spot spread deg 0 58 0 60 0 48 Scale for orientation update length 1 000 00 Frames running average for orientation update Frames between full refinements of orientation N where every Nth strong spot included in LS Figure 5 8 Integration data 11 When the integration process has finished th
9. 6 7 Structure Determination amp Refinement SMART APEX User s Manual 9 Press RETURN to choose option A The next XPREP window appears Figure 6 10 ver RIF ITO Copyright Bruker AXS 2000 Current dataset ylidim hkl Wave length Original cell 5 951 9 021 18 36 90 00 90 00 90 00 Esds 0 000 Current cell 95 9 02 8 36 90 00 90 00 Matrix 1 0000 0 0000 0 0000 0 0000 1 0000 0 0000 0 0000 0 0000 1 0000 Crystal system Orthorhombic Space group 1 2 1 2 1 t 19 chi Laue D Read modify or merge DATASETS Define unit cell CONTENTS P Contour PATTERSON sections Set up shelxtl FILES H Search for HIGHER metric symmetry 1 RECIPROCAL space displays 5 Determine or input SPACE GROUP UNIT CELL transformations 4 Apply ABSORPTION corrections Change TOLERANCES Reset LATTICE type of original cell QUIT program Select option D 4 Figure 6 10 Next XPREP window 10 Press RETURN to choose the read modify or merge datasets option D The next XPREP window appears Figure 6 11 ver 6 077Win Copyright Bruker AXS 2000 Index Data Filename or Source of Data 6860 ylidim hkl current dataset Sort MERGE current data scaling C Change CURRENT datase LINEAR scale and merge datasets W WRITE dataset to file ISOTROPIC scale and merge datasets READ in another datas Display intensity STATISTICS D DELETE stored dataset FACE indexed absorption corrections P PSI
10. Figure 4 42 8 Press Yes This completes the data collection process M86 E04015 1001 5 Datalntegration Before the data be used to solve and 3 Assign a name to the project Then use refine the crystal structure of the YLID you the built in explorer to locate the data must convert the frame data produced by directory used by the SMART program SMART to a set of integrated intensities To Figure 5 2 do so you must run the SAINT program SAINT helps you set up the SAINT input Hx pa ram ete rs Project name Integrate the data set as follows DU RETE MERE 1 Click the SAINT icon in the Bruker AXS Use the file locator to help identify frames for SAINT to process Click on a p4p or prog rams folder to start th at prog ram frame filename with the base name of the series of frames you wish to process menu recall Figure 4 1 Z Ol 2 Click Project gt New to create a new noe 2 project Figure 5 1 mus boss at Files of type files Cancel Frames path Output directory C works Figure 5 2 Assign a name and locate the directory Figure 5 1 Create a new project M86 E04015 1001 5 1 Data Integration 4 Select one of the P4P files i e not a MATRIX file from the full data set Then click open Figure 5 3 21x Project name ylid Crystal Type Protein Small Molecule Use the file locator to help identify frames for SAINT to
11. Matris Filename Output Filename C Mframes Wiid ylidl pap Browse feon C Mrames Ylidhylid1 p4p Browse Cel C Mframes lid work pli raw C Mframes pap Browse 435 C Mrames Ylidhylid2 p4p Browse Cel C Aframes lid work plid2 raw C Mtrames Vlid ylid3 p4p Browse 230 C Atrames Vlid ylid3 pap Browse Cel C Atrames vlid work ylid3 ram Browse Browse Cel Browse Browse Cel Browse Browse Cal More integration files Increment last run Count Contiguous Frames Integrate Sort Global Validate Open listing file Close Figure 5 5 Information that 5 1 has determined 7 Check to see that the values for your data set match those shown Change any parameters that do not match A resolution of 0 75 d spacing should be used for a sample to detector plane distance of 6 00 cm M86 E04015 1001 5 3 Data Integration SMART APEX User s Manual 8 Click the Integrate button to display the parameters for integration Figure 5 6 Check to see that the values for your data set match those shown Change any parameters that do not match Integrate Post integration global all data refinement Reflection size Periodic orientation matris updating v Enable periodic updating Enable global least squares refinement Limit on number af reflections to refine 3999 Constraints size degrees Y size degrees 0
12. Tools Window Help S 2 12 12 e s A 470 81 R 0 G 0 B 0 Fri 09 Jun 00 07 46 45 7 Figure 4 5 Start video frame grabber The video camera is now ready for later use Continue now to the SMART Program section of this manual M86 E04015 1001 SMART APEX User s Manual 42 Activate the SMART Program Activate the SMART program as follows 1 Double click the SMART goniometer icon to start the SMART program SMART establishes communication with the D8 controller the SMART APEX detector and the X ray generator Then it displays its main screen without unit cell information Figure 4 6 E SMART Bruker Molecular Analysis Research Tool 5 52 Copyright 1999 BrukerAXS File Edit Crystal Acquire Analyze Goniom Detector Level User Help ir wtr1oo8 4004L170 LINEAR 4004L030 512 400 Figure 4 6 Main screen without unit cell information M86 E04015 1001 Data Collection Then SMART reminds you where you last worked and displays the next message Figure 4 7 SMART 5 52 9 Last project was in sframes myulidi Return to this project Figure 4 7 Return to project 2 Press the Yes button normal response The program then informs you that it has changed directories and asks for confirmation to continue Figure 4 8 SMART 5 52 E Curent working directory is no d sframes mylidi Figure 4 8 Confirmation of current directory 4 3 Data Co
13. beam that strikes the specimen You will normally use a collimator with 0 5 mm pinholes Collimators are available ina variety of sizes depending on your application e The beam stop a hook like assembly attached to the collimator catches the remainder of the direct beam after it has passed the specimen 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 SMART APEX detector The SMART APEX detector is specific to this system It is mounted on a 20 dovetail track The track has a scale that is calibrated to indicate the distance from the crystal to the phosphor window a typical distance is 6 cm Status lamps on the detector housing indicate when the detector is on green and off red M86 E04015 1001 Hardware Overview K760 X ray generator The K760 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 SMART APEX system power settings should never exceed the maximum power rating of the X ray tube Typical maximum power settings for the SMART APEX system with a normal focus tube are 50 kV 40 mA The kV setting should not exceed 50 kV This
14. cell CONTENTS Contour PATTERSON sections Set up shelxtl FILES search for HIGHER metric symmetry RECIPROCAL space displays S Determine or input SPACE GROUP UNIT CELL transformations Apply ABSORPTION corrections Change TOLERANCES L Reset LATTICE type of original cell QUIT program Select option H Determination of reduced Higgli cell Transformation from original cell HELF matrix 1 0000 0 0000 0 0000 0 0000 1 0000 0 0 0000 0 0000 1 0000 Unitcell 960 9 03 5 3584 90 00 90 00 Niggli form 0 00 search for higher Symmetry Option FOM ORTHORHOMBIC P lattice R int Q 11 9 034 18 384 90 00 90 00 90 00 Volume Matrix 1 0000 0 0000 0 0000 0 0000 0 0000 Option B retains original cell select option Figure 6 7 YLID crystal orthorhombic primitive lattice M86 E04015 1001 6 5 Structure Determination amp Refinement 7 Press RETURN to select cell choice A The next XPREP window appears Figure BIGXPREP V5 1 Copyright 1997 Bruker AXS Current dataset vylidim rav Original cell Esds Current cell Matrix 1 0000 0 0000 0 0000 0 0000 Crystal system Orthorhombic D Read modify or merge DATASETS P Contour PATTERSON sections H Search for HIGHER metric symmetry 5 Determine or input SPACE GROUP 4 Apply ABSORPTION corrections L Reset LATTICE type of original cell option 5 Figure 6 8 Next XPREP window 6 6 90 00 1 0000
15. downweighted Enter lt CR gt to cont Figure 6 13 Next XPREP window M86 E04015 1001 6 9 Structure Determination amp Refinement SMART APEX User s Manual 13 Press RETURN to continue displaying the window The next XPREP window appears Figure 6 14 ver 6 07 Copyright Bruker Ax 5 2000 Index Dat Filename or Source of Date vylidim hkl lt current dataset ct Sort MERGE current data LIME R cale and merge datas scaling C Change CURRENT dat no sca asetas WRITE dataset to i Fh ect m B tp d m u m m ct ISOTROPIC scale and merge datasets READ in another d Display intensity STATISTICS DELETE stored data FACE indexed absorption corrections PoI scan absorption corr Copy file TRANSFORM hkl and cosines S45 SIR or SIRAS Apply HIGH low resolution cutoffs NWORMALIZE scale sigmas EXIT to main menu QUIT program Select option E li Figure 6 14 Next XPREP window 6 10 M86 E04015 1001 SMART APEX User s Manual Structure Determination amp Refinement 14 Press option E to return to the main window The following window appears Figure 6 15 ver Copyright Bruker Ax 5 2000 Current dataset ylidlm hkl Wavelength 0 71073 Chiral Original cell 5 951 g nzri 16 161 Vol Fads 0 001 0 001 Current cell 5 9 9 021 0 30 Yol 1 0000 O 0000 O 0000 0000 1 0000 O 0000 O 0000 O 0000 1 0000 Ort
16. generator is interfaced to the controller and the power settings may be adjusted either from front panel buttons or from within the SMART software Manual control module The manual control module is a remote device that you will use in certain operations to manually drive angles particularly in optical alignment of a specimen The module is physically the same as in other D8 systems but has a different keypad and functions In this application you will use only the first three rows of buttons and the AXIS PRINT button Video camera The video camera an essential part of the system allows you to visualize the crystal to optically 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 camera is mounted in the accessories track of the goniometer base 3 5 Hardware Overview 3 3 Accessories Various devices can be mounted in an accessories track on the goniometer base These include an optional low temperature attachment 3 6 SMART APEX User s Manual M86 E04015 1001 4 Data Collection We are now ready to begin actual operation of the instrument using the YLID test crystal mentioned in section 1 We assume that your system manager has set up the system properly and that all system default parameters have been set appropriately At this time double click the BrukerAXS Programs icon
17. on the Windows NT desktop Figure 4 1 dibapr 3Z dil Winzip LU LE Shorkcutto michael zip DEMO SMA Figure 4 1 Bruker AXS programs icon on desktop The BrukerAXS Programs window appears Figure 4 2 containing icons for the Bruker AXS Program modules described in Section 2 M86 E04015 1001 n L SWIHHTSProfilessAll UzerssStart Menus oil File Edit View Help T i m aL ri 7L video SMART SMART Shortcut to off line D 8tanls exe COSMO ASTRO GEMINI SAINTPLUE SHELXTL 10 abject s 4 51K B Figure 4 2 BrukerAXS programs window 4 1 Data Collection 41 Activate the Video Program Before starting the SMART program you must first activate the video camera as follows 1 Double click the Video binoculars icon recall Figure 4 2 to start the Video program and display the main window Figure 4 3 VIDEO for Windows NT File View Help oeli a Aaz As R 5 7 B Thu 08 Jun 00 09 40 54 Figure 4 3 Video program s main window 2 Click File gt New Image to open a new file Figure 4 4 VIDEO for Windows NT View Help New Image BE Open Image Ctrl 0 Recent File Exit Figure 4 4 Create new video image 4 2 SMART APEX User s Manual 3 Then press the green arrow button in the toolbox to start the video frame grabber Figure 4 5 VIDEO for Windows NT Imagel File Edi Grab View
18. phi by 180 and to verify that you have correctly centered the sample at both o 0 and 180 Do not be concerned if the crystal moves away from its center as it rotates you have not yet adjusted the Y axis Note Hepeat this process as many times as necessary Each time you press the A button the phi angle will rotate between 0 and 180 7 Pressthe B button to rotate the phi angle to 90 for adjustment of the Y axis Fig 4 25 4 10 SMART APEX User s Manual VIDEO for Windows NT Imagel Djaja zzz gt a _ ale Figure 4 25 Crystal oriented for Y axis adjustment 8 Adjust the goniometer head s Y axis adjustment screw Figure 4 19 to center the crystal on the crosshairs intersection Figure 4 26 VIDEO for Windows NT Imagel Figure 4 26 Crystal centered on crosshairs 90 M86 E04015 1001 SMART APEX User s Manual 9 Press the B button again to rotate the phi angle to 270 and to verify that you have correctly centered the sample at both 90 and 270 Note Repeat this process as many times as necessary Each time you press the B button the phi angle will rotate between 90 and 270 The center of mass of a properly aligned specimen should stay in the same place with respect to the center of the crosshairs in all angle settings Note If the video camera has become misaligned the center of the crosshairs may need to be adjusted by
19. when handling the goniometer head to prevent damage to your expensive sample on the end of the small glass fiber Carefully remove from its case the goniometer head containing the YLID test crystal Place the goniometer head onto its base on the phi 6 drive aligning the head s key slot with the key pin in the base Snugly screw the head s collar to the base such that the head does not move but do not overtighten it Note At 920 the key on the mounting base of the goniometer head will be at the 12 00 position M86 E04015 1001 Data Collection 13 Click Crystal Generator to check the X ray power The Goniometer Generator Options panel appears Figure 4 18 kV 50 mA 30 Wait Y N Check for yes cn Figure 4 18 Goniometer Generator Options panel 14 Set appropriate values for kilovolts kV and milliamps mA For this experiment we want 50 kV and 30 mA Click OK to program these new settings 4 3 Optically Align the Sample To obtain accurate unit cell dimensions and to collect good quality data you must align the center of the sample with the center of the X ray beam and maintain the alignment for the entire experiment We assume that your video camera has been aligned so that the crosshairs of the video camera coincide with the center of the goniometer and the center of the X ray beam 4 7 Data Collection Align the sample as follows 1 Click Crystal Evaluate to begin the al
20. with beam stop e SMART APEX detector e K760 X ray generator e Manual control module e Video camera Goniometer with fixed chi stage The standard SMART APEX system uses a horizontally oriented D8 PLATFORM goniometer base with 2 theta 20 and omega o drives with dovetail tracks for the X ray source and the detector and mounting posts for accessories such as the video camera and optional low temperature attachment The system also incorporates a fixed chi stage Incident Beam Collimator Beam Stop Fixed Chi Stage Head SMART APEX Detector System ___ SMART Rotary Shutter amp Attenuator Assembly Safety Shutter Sealed X ray Tube ee D8 Goniometer Graphite Crystal Monochromator Figure 3 2 SMART APEX amp goniometer module instrumentation M86 E04015 1001 3 3 Hardware Overview with chi angle of approximately 54 74 and a phi drive with 360 rotation All four axes 20 and intersect within a volume of approximately 10 microns These axes are shown in Figure 3 3 axis B Figure 3 3 Fixed 3 axis goniometer 3 4 SMART APEX User s Manual X ray source Three components Figure 3 2 comprise the X ray source a shielded X ray tube an X ray safety shu
21. your system manager 10 Cycle between the two positions of both A and B one last time to ensure that the crystal remains centered in all positions 11 After the alignment has been completed using and B positions you should verify the alignment by using the C and D buttons in a similar manner 12 When you have completed the optical alignment steps remove any paper you might have placed on the detector face and close the doors of the enclosure 13 Click on the SMART program window then press the ESC key to exit the optical alignment stage SMART then prompts for a rotation photograph Figure 4 27 M86 E04015 1001 Data Collection SMART Bruker Molecular Analysis Research Tool 5 52 Copyright 1999 YLID1 taDir s ylid1 5 1141 Distance FloodFld 40041170 Spati LINEAR Dark 4004L010 Size Spd 512 400 Figure 4 27 Prompt for a rotation photograph 14 Press Y normal response SMART will then perform a 60 second rotation photo During this time phi data on the screen will be highlighted and the shutter data will read OPEN Upon completion of the photo the image frame will display on the screen Figure 4 28 SMART Bruker Molecular Analysis Research Tool 5 52 Copyright 1999 BrukerAXS File Edit Crystal Acquire Analyze Goniom Detector Level User Help YLID Test Crystal rotation 03 05 00 17 39 47 Created 03 05 00 a 0 0000 Distance 5 984 Flood
22. 23 128 parameters GooF 5 0 590 Restrained GooF 0 590 for restraints R1 0 0505 for 2231 Fo gt Azig Fo and 0 0518 for all 2332 data wR 0 1382 Goof 5 0 590 Restrained GooF 0 590 for all data R1 0 0535 for 1407 unique reflections after merging for Fourier Highest peak 0 51 at 0 3138 0 5738 0 2321 0 96 A from C10 Deepest hole 0 24 at 0 1814 0 8834 0 1210 1 30 from C2 FEE ia sis sis EEE EEE EEE EEE EEE EEE EEE EEE EEE EEE EEE EEE EEE EEE EEE tt ttt viidim finished at 08 09 31 Total elapsed time 3 0 secs FEE ia sis sis EEE EEE EEE mia sis sis sis sis sis sis EEE EEE EEE EEE EEE EEE EEE EEE is sis sis sis mia mia sis mia ais sis sis sia sia ttt tt Print Figure 6 31 Least squares refinement In the output above note that the R1 value is 5 0 This is typical for a preliminary anisotropic refinement with no H atoms included 6 22 M86 E04015 1001 SMART APEX User s Manual Structure Determination amp Refinement 37 Click OK to return to XSHELL 38 Kill the Q peaks as before Then click Atoms gt Hybridize All Figure 6 32 The atoms will appear in different colors plid m res File Edit Hefe Select View Preferences Labels Render Help Edit Soot Info an All Info on Selected Plane Weighted Plane Grow Pack Trim EMOL Hybridize All Calculate Hydragens Figure 6 32 Hybridize all M86 E04015 1001 6 23 Stru
23. 600000 Z size degrees 0 300000 v Use narrow frame algorithm Periadic updating frequency Constraints v Constrain refinement by Laue class Crystal system Orthorhombic a b c 90 90 90 Detector center Detector center Y Detector pitch Detector roll Detector yaw Detector distance Unit cell axes Unit cell angles jw Constrain integration by Laue class Crystal system Orthorhombic a b c 90 90 90 Detector centers Detector center Y Detector pitch Detector roll Detector yaw Detector distance Unit cell axes Unit cell angles Goniometer zeros M Crystal translations IM Enable box size optimization Decay correctian Apply decay correction Goniometer zeros M Crystal translations More integration options Post integration sorting and Filtering Sort by Laue class Point group mmm orthorhombic Minimum sigmal to output 3 000000 W Enable correlation filter Continuous crystal and detector arientation updating v Enable continuous updating Integration Files Advanced Integrate Damping factor P 2R dcs fi 000000 Integrate Sort Global Validate Open listing file Figure 5 6 Integrate input window 5 4 M86 E04015 1001 SMART APEX User s Manual 9 Click the Advanced Integrate button to display the Advanced Integrate input box Figure 5 7 Compare the values for your data set with those shown Make r
24. 7 Max shift 0 006 A for Max dU 0 001 for C10 WR 0 06 73 before cycle 3 for 2435 data and 130 7 130 parameters GooF 5 0675 Restrained GooF 0 675 for restraints Mean shiftfesd 0 073 Maximum 4 817 for EXTI at 17 01 07 Max shift 0 001 A for 10 Max dU 0 000 for C10 WR 0 0873 before cycle 4 for 2435 data and 130 7 130 parameters GooF 5 0 676 Restrained GooF 0 676 for restraints Mean shiftfesd 0 045 Maximum 4 814 for EXTI at 17 01 08 Max shift 0 001 A for Max dU 0 000 for 01 wR 0 0873 before cycle Sfor 2435 data and 130 parameters GooF 5 0675 Restrained GooF 0 675 for restraints R1 0 0316 for 2297 Fo gt 4sig Fo and 0 0334 for all 2435 data wR O 0673 Goof 5 O 675 Restrained Goof 0 575 for all data R1 0 0326 for 1436 unique reflections after merging for Fourier Highest peak 0 29 at 0 8214 0 4402 0 1532 0 72 A from C1 Deepest hole 0 17 at 01898 O 4771 0 0215 1 28 A from T EHE HE HE HE HE HE HE HE HE HE HE HE HE HE HE HE HE HE HE HE HE HE HE HE HE HE HE HE HE HE HE HE HE HE HE HE HE HE HE HE HE HE HE HE HE HE HE HE HE HE HE HE HE HE HE HE HE HE HE HE HE HE HE HE HE HE HE HE HE HE HE HE HE HE H LIDim finished at 17 01 09 Total elapsed time 3 6 Secs THEE EEE EEE sis sis sis ia sis sis mis sia sis sia mi is mis sia mis sia sis ia mi sis ais sia sis sis sis mia mis sis sis si mis sis mis is sis sis sis mis sis mia sis sia sis mia mis s
25. ERE Li Fr Suggested 0 151300 Iv 1 313100 Iv BEEN EE Program Priority C Ide Normal High Realtime Cancel Figure 6 30 Refinement control 35 Change the input values to include Extinction and Anisotropic refinement Also reduce the number of difference peaks to 5 If the refinement indicates an inverted structure as in our example also check the Invert box 6 21 Structure Determination amp Refinement SMART APEX User s Manual 36 Click OK to launch the XL least squares refinement program Figure 6 31 Hefine Mean shifl esd 1 557 Maximum 11 250 for U13 51 at 08 09 29 gt Max shift 0 020 for C5 Max dli 0 002 for C2 wR 0 1614 before cycle 2 for 2332 dala and 1287 126 parameters GooF 5 0 697 Restrained GooF 0 697 for restraints Mean shifl esd 1 439 Maximum 11 279 for U13 51 at 08 09 30 Max shift 0 006 A for C5 Max dU 0 003 for C5 WR 0 1393 before cycle J for 2332 data and 1287 128 parameters GooF 5 0 596 Restrained GooF 0 596 for restraints Mean shifl esd 0 331 Maximum 2 923 for at 08 09 30 Max shift 0 002 A for C10 Max dU 0 001 for C5 WR 0 1383 before cycle 4 for 2332 data and 128 126 parameters GooF 5 0591 Restrained GooF 0 591 for restraints Mean shifl esd 0 081 Maximum 2 917 for EXTI at 08 09 31 Max shift 0 001 for C5 Max dU 0 000 for C5 wR 0 1382 before cycle 5 for 2332 data and
26. Fld 4004L170 Spatial LINEAR k 4004L010 Dar Size Spd 512 400 Figure 4 28 Image frame following 60 second rotation At this time proceed to Unit Cell Determination Data Collection 4 4 Unit Cell Determination Perform a unit cell determination as follows 1 From the SMART program click Crystal Unit Cell The following message appears asking you to verify that the distance and beam center are correct Figure 4 29 SMART 5 52 CONFIGURE EDIT Distsc rc 6 0 261 1 250 5 le this correct Figure 4 29 Distance and beam center verification 2 Ensure that the distance shown on the detector scale agrees with the value shown on the screen Then press Yes SMART then displays a set of default values for unit cell determination and asks you to confirm them Figure 4 30 Options for Crystal gt Unit Cell it Frames Frame width 0 3 Seconds frame 10 Title Unit Cell Determination Job name matrix Max display counts 1 Lower axial limit 3 0 Upper axial limit 200 0 Indexing HKL tolerance 0 2 LS RLY tolerance 0 01 Cancel Figure 4 30 Set of default values for unit cell determination 4 12 SMART APEX User s Manual Press OK as these values are appropriate for this crystal The program then collects three sets of 20 frames called MATRIXO MATRIX1 and MATRIX2 Figure 4 31 nalysis Research Tool V5 52 Copyright 1999 BrukerAXS Gonion Detector bevel User Unit Cell Determinati
27. Press the A button on the manual control TEE s module to drive the goniometer angles to ln c the base position 20 30 30 _ Sample Z axis Lock and O for optical alignment Mounting Collar Note If you have difficulty seeing the image of the crystal you may want to Screw better illuminate the sample with a high intensity lamp and or temporarily place a aos oe light colored piece of paper on the front of Du justment P Screw the detector 4 Adjust the goniometer head s Z axis Screw X axis Lock adjustment screw recall Figure 4 21 until the crystal is near the crosshairs intersection on the video screen Figure 4 23 X axis Lock Figure 4 21 Goniometer head adjustment locations VIDEO for Windows NT Imagel 2 Click on the Video window to display the real time image of the crystal Figure 4 22 VIDEO for Windows NT Imagel 21212 la gt Alv 1 Figure 4 23 Crystal near the crosshairs intersection Figure 4 22 Real time image of the crystal M86 E04015 1001 4 9 Data Collection 5 Adjust the goniometer head s X axis adjustment screw to center the crystal on the crosshairs intersection Figure 4 24 VIDEO for Windows NT Imagel Djela S m Ota AL Figure 4 24 Crystal centered on crosshairs 0 6 Pressthe A button again to rotate the
28. am Priority C 19 Normal C High Realtime Cancel Figure 6 27 Refinement control M86 E04015 1001 Structure Determination amp Refinement SMART APEX User s Manual 31 Click OK to launch the XL least squares refinement program Figure 6 28 Refine GooF 5 2 372 Restrained GooF 2 372 for restraints Mean shiftfesd 24398 Maximum 11 246 for 011 51 at 16 42 09 Max shift 0 040 A for C4 Max dli 0 006 for C1 wR2 0 2582 before cycle 3 for 2435 data and 577 57 parameters 5 2 065 Restrained Goof 2 065 for 0 restraints Mean shifl esd 0 330 Maximum 2 089 for x at 16 47 09 Max shift 0 012 for C4 Max dU 0 000 for C5 WR 0 2574 before cycle 4 for 2435 data and 577 57 parameters GooF 5 2 152 Restrained Goof 2 052 for 0 restraints Mean shiftfesd 0 128 Maximum 0 501 for x O2 at 16 47 09 Max shift 0 003 A for Max 0 000 for WR 0 2575 before cycle 5 for 2435 data and 7 Sf parameters GooF 5 2 052 Restrained GooF 2 052 for restraintz R1 0 0883 for 2297 Fo gt 4sig Fo and 0 0917 for all 2435 data WR 0 2575 GonF 5 2152 Restrained Goof 2 052 for all data Absolute structure probably wrong invert and repeat refinement R1 0 0933 for 1436 unique reflections after merging for Fourier Highest peak 1 03 at 0 257656 0 3357 0 24298 0 50 from 51 Deepest hole 0 64 at 0 1642 2805 0 2391 0 53 A from 51
29. ay be stored in a retrieval system transmitted or reproduced in any way including but not limited to photocopy photography magnetic or other record without prior written permission of Bruker AXS Inc Address comments to Marketing Communications Department Bruker AXS Inc 5465 East Cheryl Parkway Madison Wisconsin 53711 5373 USA Note 1 Windows NT is a registered trademark of Microsoft M86 E04015 1001 Table of Contents 1 Jdntroduc HOT 0526017229 ed owus TENERE UE 1 1 1 4 SMART APEX Features 1 1 1227 Se MORS BS ASI m 1 1 2 FOTW AS OVervieW eranc dana E 2 1 3 Hardware 3 1 SMART APEX System GOImDOTDGF ES dtt tct 3 1 3 2 Q3 axis Goniometer Module with SMART APEX 3 3 33 eere i i 3 6 4 Data 4 1 4 1 Activate the Video 4 2 4 2 Activate the SMART
30. cture Determination amp Refinement SMART APEX User s Manual 39 Click Atoms Calculate Hydrogens Figure 6 33 ylid1 m res File Edit Aefine Select View Preferences Labels Render Help Info en All Info on Selected Plane Weighted Plane Hybridize All Calculate Hvdragens Figure 6 33 Calculate hydrogens 6 24 M86 E04015 1001 SMART APEX User s Manual Structure Determination amp Refinement 40 The 10 H atoms will be added Figure 6 34 vlidim res File Edit Refine Select Atoms View Preferences Labels Render Help Figure 6 34 Ten H atoms added M86 E04015 1001 6 25 Structure Determination amp Refinement SMART APEX User s Manual 41 Click the Refine button at the top of the XSHELL Menu A panel will appear Figure 6 35 Refinement Control 3 EA Difference Map e m m m EL r Fr pum poem E Figure 6 35 Refinement control 6 26 M86 E04015 1001 SMART APEX User s Manual Structure Determination amp Refinement 42 Click OK to launch the XL least squares refinement program Figure 6 36 Mean shiftfesd 1 161 Maximum 5 496 for C4 at 17 01 06 Max shift 0 072 A for Max 0 001 for C4 wR 0 0686 before cycle 2for 2435 data and 1307 130 parameters GooF 5 0 686 Restrained GooF 0 686 for restraints Mean shiftfesd 0 525 Maximum 4 775 for EXTI at 17 01 0
31. e Kill Selected button in the Select carbon atoms 9 atoms in fused 5 amp 6 menu The peaks will disappear Figure membered ring 2 atoms attached to S 6 21 atom in the order in which they are to be numbered ylid1 File Edit Refine Select Atoms View Preferences Labels Aender Help Figure 6 21 Peaks disappear M86 E04015 1001 6 17 Structure Determination amp Refinement 25 Click Labels Group Label Figure 6 22 m res File Edi Refine Select Atoms View Preferences MINES Render v Labels v Hydrogen Labels Hybrid Label Coloration Turn Selected Atom Labels Off Tum Selected Atom Labels On Group Label Find Duplicate Labels Figure 6 22 Select Group Labels A panel will appear to label these peaks Figure 6 23 Initial Number Note Leave empty any field which you da nat with changed Also Ascending Order E Descending _ the program will 200 p truncate any label over Trailer 4 characters long L 1 Figure 6 23 Input panel 6 18 SMART APEX User s Manual 26 Click OK to label these peaks as C with a starting number of 1 Figure 6 24 ylid1 m res olx File Edit Refine Select Atoms View Preferences Labels Render Help Figure 6 24 Label the peaks 27 Select the two remaining atoms Then click Labels gt Group Label again and click
32. e results of the global refinement of unit cell parameters display Figure 5 9 2 C SAXIASAINT 32 SAINT exe Performing final unit cell least squares on file D frames ylidi work YLID11 _ma i i 5346 reflections ne reflection will be stored in memory per 1 reflections read Performing orientation least squares 5346 reflections rientation UB matrix 0 1130234 0 0217837 0 0389220 0 0017302 0 1067011 0 0149414 0 1245285 0 021253 0 0351184 B C Alpha Beta 5 9460 9 0125 18 3448 90 000 90 000 0 0004 0 001 0 001 orrected for goodness of fit 0 0003 0 0005 0 0010 0 001 0 001 Range of reflections used Worst res Best res Min 2Theta Max 2Theta 9 1724 0 7496 4 441 56 600 rystal system constraint 5 Orthorhombi c Parameter constraint mask 512 Eulerian angles 68 999 49 891 104 504 oniometer zeros deg 0 0000 0 1185 0 0000 0 0013 rystal translations pixels 0 0000 0 0000 0 0000 etector corrections X Cen Dist Pitch Roll Yaw 0 721 0 097 0 013 0 332 0 305 0 210 Refinement statistics StartingRes FinalRes GOF Cycles Code 2 04334E 05 2 34486E 04 1 46 3 New orientation is in D frames ylidi work YLID1Im p4p End final global unit cell least squares refinement 08 08 00 13 48 31 Press ENTER to continue Figure 5 9 Integration summary 5 6 M86 E04015 1001 SMART APEX User s Manual Data Integration 12 Before pressing the Enter key scroll up the screen to displa
33. ections and the unit cell parameters with errors Figure 4 39 Least Squares Output x Orientation Matrix 0 00213029 0 10657495 0 01467802 0 11297587 0 02116330 20 03880606 0 12384082 0 02113986 0 03514899 Lattice parameters amp Standard deviations 5 9650 90 0 9 0340 18 3903 00 90 000 90 000 0 0008 0 0032 0 0046 0 021 0 018 0 021 0 50 Standard deviations corrected for 0 0008 0 0033 0 0047 0 022 0 018 0 022 0 52 Histograms H 82 K 82 I 82 Onega 81 Wil Wee aL abs al tl eS A ee dues X 49 26 7 0 0 0 0 0 0 0 Y 75 z7 0 0 0 0 0 0 0 0 K Onega X Y Figure 4 39 Histogram for reflections and unit cell parameters with errors If the refinement process was done correctly the histogram will show zeros in all columns except the first 4 Press OK A message asking you to overwrite the default file for refined unit cell parameters matrixO p4p appears Figure 4 40 SMART 5 52 2 Overwrite d frames wlid1 smatrms p p Figure 4 40 Overwrite default matrixO p4p file 5 Press Yes You have now completed the least squares refinement process 4 16 SMART APEX User s Manual 6 Click File Exit to leave the SMART program The exit message appears Figure 4 41 SMART v5 52 2 EXIT you sure Figure 4 41 7 Press Yes The save message appears Figure 4 42 SMART v5 52 2 Save the current configuration
34. ed is a brief description of each component as well as options available with the system Section 4 Data Collection describes basic operation of the hardware and software of the SMART APEX system to collect single crystal X ray diffraction data Procedural steps are presented in a typical fashion that you would use to analyze an unknown sample Section 5 Data Integration explains how to convert the raw frame data to a set of integrated intensities that can be used to solve and refine the crystal structure This section will illustrate use of the SAINT interface program to carry out integration of a data set previously collected in Section 4 Section 6 Structure Determination amp Refinement demonstrates how to use the reduced intensity data to produce a crystal structure The SHELXTL suite of crystallographic programs will be described SMART APEX User s Manual Examples in this manual use the specimen sample 2 dimethylsulfuranylidene indan 1 3 dione YLID similar to the crystal provided with your system By using a similar sample you can duplicate the procedures described in this manual and obtain similar results to assure your understanding of the SMART programs That is your results should match those outlined in this manual except for minor variations caused by slight differences in specimens or instrument parameters Note Before using this manual ensure that the system is in proper working condition e g
35. equired changes Advanced Integrate profiles Pi igma lower limit Far reflections used to update model profiles JL Fraction of model profile maximum used ta generate simple sur limits 0 050000 Pera signa threshold for least squares fit below vs simple sum above 8 000000 8999 0000 Resolution lower limit above which simple sum is always used Blend 9 profiles Background and Active Mask Base 2 log of background update scaling factor X b b XN jo Use pre existing active pixel mask Fractional lower limit to generate active mask fraction of average intensity 0 000000 Active mask am file Browse Spatial correction Apply spatial calibration correction from separate indexed fiducial ix file Browse verde selected input frame header information Overide frame header Scan axis Frame width theta mega Chi Integrate Sort Global Validate Open listing file Figure 5 7 Advanced Integrate input window Spatial _ 1 file M86 E04015 1001 Data Integration Beam monitor synchrotron systems Enable beam monitor normalization Normalize all runs ta the first detectors Enable reference correction Output listing and diagnostic files Generate diagnostic plot files Keep temporary files Append listing file Verbosity of listing file 1 24 100
36. for 2435 data and 1307 130 parameters GooF 5 1 025 Restrained GooF 1 025 for 0 restraints Mean shififesd 0 043 Maximum 3 930 for EXTI at 17 09 08 Max shift 0 000 A for 1 Max dU 0 000 for WR 0775 before cycle 4 for 2435 data and 1307 130 parameters GooF 5 1 026 Restrained GooF 1 026 for 0 restraints Mean shififesd 0 033 Maximum 3 929 for EXTI at 17 09 09 Max shift 0 000 A for H10C Max dU 0 000 for C7 wWR2 0 0776 before cycle 5 for 2435 data and 2 1 130 parameters GooF 5 1 025 Restrained GooF 1 025 for 0 restraints R1 0 0309 for 2297 Fo gt 4sig Fo and 0 0326 for all 2435 data WR 00776 GooF S 1 025 Restrained GooF 1 075 for all data R1 0 0317 for 1436 unique reflections after merging for Fourier Highest peak 0 26 at 0 7701 0 3558 0 2036 0 82 A from C1 Deepest hole 0 18 at 0 1900 0 4769 0 0242 1 30 A from THEE HE EEE EEE EEE EEE dE EE EEE GE dE GR EE EE GR REGERE GEHE GR REGERE GR GE EG tt ttt GG vlidim finished at 17 09 09 Total elapsed time 3 3 secs TEE EHE HE HE HE HE E EHE GEHE HE GEHE EE EE dE HE HERE EHE EE dE GE GEHE dE sia sis sia sis sis sis sis sis sis mis sis sis sis sis is sis mis sis sia sis sia sis sia sis is sis sia sia sis tt ttt Figure 6 38 Least squares refinement In the output above note that the R1 value is 3 1 and that the goodness of fit GooF value is now 1 026 We have carried out a complete refinement of suitable qual
37. horhombic Space group 2 112111211 19 Read modify or merge DATASETS C D etine unit cell CONTENTS Contour PATTERSON sections F Set up shelxtl FILES R RECIPROCAL space displays U UNIT CELL transformations ABSORPTION corrections T Change TOLERANCES LATTICE type of original cell 2 QUIT program Select option li Figure 6 15 Next XPREP window M86 E04015 1001 6 11 Structure Determination amp Refinement SMART APEX User s Manual 15 Press RETURN to choose the Define Unit Cell option C The unit cell contents will be summarized on the next menu Figure 6 16 v BIGXPREP V5 1 Copyright c 1997 Bruker AXS Current formula is C11 H10 02 5 Tentative 2 number of formula units cell O giving rho 1 364 non H atomic volume 17 7 and following cell contents and analysis 44 00 64 05 5 H 40 00 4 89 5 8 00 15 52 4 00 15 54 4 change 2 new FORMULA R change RADIATION E EXIT to main menu or Q QUIT program Figure 6 16 Summarized unit cell contents 6 12 M86 E04015 1001 SMART APEX User s Manual 16 If you did not enter the chemical formula when you created the new project for the YLID crystal in the SMART program you must do so now The correct chemical formula for the YLID crystal is C11 H10 O2 S If the information is correct press RETURN to display the next window Figure 6 17 BIGXPREP V5 1 Copyright 1997 Bruker AXS Current datase
38. i sis sis sis sis sia sia sis mis ttt Figure 6 36 Least squares refinement In the output above note that the R1 value is 3 2 This is typical for an anisotropic refinement with H atoms included M86 E04015 1001 6 27 Structure Determination amp Refinement SMART APEX User s Manual 43 Click OK to return to XSHELL and delete Q peaks 44 Click the Refine button at the top of the XSHELL Menu A panel will appear Figure 6 37 Mean shifl esd 1 161 Maximum 5 496 for y C4 at 17 01 06 Max shift 0 072 A for HTOUB Max dl 0 001 for C4 wR 0 0885 before cycle 2 2435 data and 130 130 parameters GooF 0 636 Restrained GooF 0 686 for restraints Mean zhifl ezd 0 525 Maximum 4 775 for EXTI at 17 01 07 Max shift 0 008 A for Hi0B Max 0 001 for wR 0 0873 before cycle 3 for 2435 data and 130 7 130 parameters GooF 5 0 675 Restrained Goof 0 675 for 0 restraints Mean zhifl ezd 0 073 Maximum 4 817 for EXTI at 17 01 07 Max shift 0 001 A for Max dl 0 000 for wR2 0 0873 before cycle 4 for 2435 data and 1307 130 parameters GooF 5 0 676 Restrained GooF 0 676 for restraints Mean shififesd 0 045 Maximum 4 814 for EXTI at 17 01 08 Max shift 0 001 A for Max dU 0 000 for wi 0 0873 before cycle Sfor 2435 data and f 130 parameters GooF 0 675 Restrained Goof 0 675 for restraints R1 0 0316 for 2297 Fo gt 4sig F
39. ignment of the sample in the center of the X ray beam The alignment process combines optical alignment steps with rotational photo steps The menu bar at the top of the SMART screen remains gray Figure 4 19 until you complete the optical alignment step and exit by pressing the ESC key SMART Bruker Molecular Analysis Research Tool 5 52 Copyright 1999 BrukerAXS File Edit Crystal Acquire Analyze Goniom Detector Level User He Project YLID1 DataDe DataDir s ylidl wor noe 1 s ylidl 2 Theta ce s FloodFld 40041170 Spatial LINEAR Dar 4004L010 Size Spd 512 400 anual Mode Esc Exit S Shutter T Atten A Add C Count U Status Figure 4 19 Grayed SMART screen menu bar during optical alignment SMART APEX User s Manual During the first stage optical alignment you will control the instrument from the manual control module Figure 4 20 using buttons A and B Figure 4 20 Manual control module Also during optical alignment you will adjust the goniometer head at screw locations shown in Figure 4 21 Use the goniometer wrench to unlock the axis adjustment locks and later lock them Use the other end of the wrench to turn the adjustment screws M86 E04015 1001 SMART APEX User s Manual Data Collection 3
40. ing run 9999 Oscillate Checkfor yes Figure 4 33 Data collection options 4 14 SMART APEX User s Manual 2 Enter the job name then press OK to begin data collection Figure 4 34 SMART Bruker Molecular Analysis Research Tool 5 52 Copyright 1999 BrukerAXS File Edit Crystal Acquire Analyze tector level User YLID Test Crystal YLID11 003 03 05 00 18 04 4 Phi Chi Distance 5 984 FloodFld 40041170 Spatial LINEAR Dark 4004L010 E p EST T 512 400 ollecting YLID11 004 Disk Kb 1560620 Time used left 0 00 43 5 18 05 Figure 4 34 Data collection The hemisphere data set specified in this example will require about four hours to collect Upon completion of data collection the following message displays Figure 4 35 SMART 5 52 N more runs in EditRuns array Figure 4 35 No more runs in Edit Runs array M86 E04015 1001 SMART APEX User s Manual 3 Press OK Then click Goniom Zero to drive the goniometer angles to zero The following drive message appears Figure 4 36 SMART v5 52 2 Drive all angles to zero are you sure Figure 4 36 Drive all angles to zero 4 Press Yes 4 6 Least Squares Refinement Before leaving the SMART program you might want to improve the orientation matrix that will be used for integration Do so as follows 1 Click Crystal LS to further perform the least squares refinement The Least Squares Optio
41. ity for publication This is typical for a final anisotropic refinement with H atoms included M86 E04015 1001 6 29 Structure Determination amp Refinement SMART APEX User s Manual 46 Click OK to return to XSHELL 47 To display the thermal ellipsoids for the final structure click on the background with the right mouse button and select Thermal Ellipsoids Figure 6 39 ylidi mres File Edit Refine Select Atoms View Preferences Labels Aender Help Figure 6 39 Thermal Ellipsoids 6 30 M86 E04015 1001
42. l has been displayed handshaking Chemical Formula cC11 H10 02 5 finished the menu headings return to Crystal Morphology Sphere r Crystal Color Pale Yellow black active Maximum Dimension 0 36 Intermediate Dimension Click Crystal gt New Project to start a new project A new project options window appears Figure 4 10 Minimum Dimension Collection Temperature Measured Density Density Method 23 d framestylid1 d framest ylid1 Check for yes Working Directory Data Directory Backup Work Directory cme Figure 4 11 Options window 4 4 M86 E04015 1001 SMART APEX User s Manual Data Collection The following save message appears Figure 4 12 PROJECT DEFAULTS SMART 5 52 Small Molecule Figure 4 12 Save the current configuration 6 Press Yes Another message prompts you to create the new directory Figure 4 13 The message will appear twice if the working directory and the data directory are not the same SHART 5 52 e Figure 4 14 Project defaults we Figure 4 13 Create the new directory 7 Click Yes normal response SMART then asks you to load the system default settings Figure 4 14 M86 E04015 1001 4 5 Data Collection SMART APEX User s Manual 8 Select Small Molecule then press OK 9 Click Level Level1 Figure 4 16 This SMART loads the system defaults and level has a minimum number of options displays a SMART screen This scree
43. l the refined solution goes to name RES convergence XSHELL name RES Final Solution XSHELL name CIF 3 XCIF name PCF Figure 6 1 Flow chart M86 E04015 1001 name LS name PRP name PCF name LST name LST name CIF name FCF name PLT name ORT name TBL name SFT Data Collection and Data Reduction Data Reduction Space Group Determination and Absorption Correction Generate Trial Solutions Analysis of Trial Solutions Structure Refinement Analysis of Refined Solutions Final Plots for Publication Final Tables for Publication required to begin the structure solution and refinement process The various steps in solving and refining the structure are carried out using the programs of the SHELXTL package A simplified flow chart is shown in Figure 6 1 Structure Determination amp Refinement Solve and refine the crystal structure as follows 1 Click the SHELXTL icon in the Bruker AXS folder to start SHELXTL recall Figure 4 2 2 Click Project New to create a new project for the YLID Figure 6 2 CO Shelxtl Program and Project Manager 589 XPREP xS XSHELL XL XP xwAT XPRO XCIF XF0G XxPOW XPS Edi Help Figure 6 2 Create a new project SMART APEX User s Manual Use the built in Explorer to locate the YLID1m raw file In this example the file is in D frames ylid1 work Figure 6 3 pen a New Project Project name Dim
44. llection Press OK normal response The ptions for Crystal New Project SMART APEX User s Manual Crystal 32 X chars program then communicates with the die instrument then loads the calibration files usen init parameters from the previous project Crystal Color Figure 4 9 Intermediate Dimension Minimum Dimension SMART Bruker Molecular Analysis Research Tool 5 52 Copyright 1999 BrukerAXS Manei Eie Edit EEF Acquire Analyze Goniom Detector 9 User Help Measured Density i Density Method Working Directory Data Directory Backup Work Directory Check for yes RA Figure 4 10 New project options window after entering rojec my 11 MENTIS C information d 5 Fill in all available information as shown Figure 4 11 Note that you must specify a Project Name lines 1 and 2 and a Working Directory and a Data Directory which may be the same You should also enter additional information specific to your specimen so that it will appear in the final structure report When you are finished click OK Options for Crystal gt New Project Distance 5 FloodFld 40041170 Spati al LINEAR Dark 4004L060 Size Spd 512 400 Figure 4 9 Screen showing data from previous project Note While presenting data handshaking the menu headings Crystal 32 chars YLID appear grayed inactive Once all data a tata Title YLID Test Crysta
45. n for routine problems such as YLID and Will contain the sample to detector plane will be used for this tutorial experiment distance the current goniometer angle Level2 has more crystallography options settings current dark and flood files and required for special problems Level3 is information concerning your project and designed for use by a system manager its working and data directories No unit only cell information displays Figure 4 15 SMART Bruker Molecular Analysis Research Tool 5 52 Copyright 1999 BrukerAXS File Edit Crystal Acquire Analyze Goniom Detector 828 User SMART Bruker Molecular Analysis Research Tool 5 52 Copyright 1999 BrukerAXS File Edit Crystal Acquire Analyze Goniom Detector Level User Help v Level 1 Ctrl 1 Level 2 Ctrl 2 Level 3 Ctrl 3 Command Line Ctrl K Project YLID1 DataDe DataD1 v A ataDir s ylid1 WorkDev d WorkDir s ylidi Figure 4 16 Level menu 2 Theta Omega Phi Figure 4 15 SMART screen with loaded data 4 6 M86 E04015 1001 SMART APEX User s Manual 10 Click Goniom Zero to drive all angles to zero and check the goniometer scales to ensure that all angles read zero The following drive message appears Figure 4 17 SMART v5 52 E 2 Drive all angles to zero are you sure Figure 4 17 Drive all angles to zero The system is now ready for you to begin the experiment 11 12 CAUTION Use extreme care
46. nics and firmware for driving goniometer angles opening the X ray shutters and monitoring other instrument functions such as safety interlocks generator status and detector statuses 3 2 SMART APEX User s Manual Refrigerated recirculator for SMART APEX detector The refrigerated recirculator uses Peltier technology to cool the CCD chip to a required 40 C to minimize dark currents Computer Included with the system is a high speed computer which is used for control of the experiment storage of raw frame data integration of data and solution and refinement of the structure The computer uses the Microsoft Windows NT operating system and includes the software described in Section 2 Often the computer is attached to a network of similarly configured computers with access to local and or network printers M86 E04015 1001 SMART APEX User s Manual 3 2 3 Goniometer Module with SMART APEX Detector The 3 axis goniometer module and its associated SMART APEX detector comprise the unique hardware of the SMART APEX system This is the part of the instrument that actually performs the experiment Several components comprise the 3 axis goniometer module with SMART APEX detector Figure 3 2 e Goniometer with fixed chi y stage e X ray source including shielded X ray tube X ray safety shutter and graphite crystal monochromator Hardware Overview e SMART rotary shutter and incident beam collimator
47. ns window appears Figure 4 37 M86 E04015 1001 Data Collection Least Squares ptions center at 261 5 254 2 of a 512x512 frame Output file matrix0 p4p Constraint 5 Ortho Max RLY error 0 01 Constraint mask 512 Unit Cell axis B axis 005 axis 18 404 Alpha Beta 90 000 Gamma 90 000 Detector Corrections Xbeam center 0 093 Y beam center 0 008 Distance cor 0005 Detector pitch 359 Detector roll 0388 Detector yaw 0 240 Eulerian angle 1 68 886 Eulerian angle 2 50 01 Eulerian angle 3 1 04 522 Crystal X trans 0 0000 Crystal Y trans 0 0000 Crystal Z trans 0 0000 Omega zero 0 0590 Chi zero o Frame halfwidth 0 1 5 0 000 1365 Figure 4 37 Least Squares Options window The YLID crystal is orthorhombic and therefore the alpha beta and gamma angles should be 90 You may constrain them to be so with the Constraint field of the Least Squares Options window 2 Change the Constraint field to Ortho and press OK The program may remove a few of the poorest fitting reflections The following removal message appears Figure 4 38 SMART V5 52 x 2 3 reflection s removed from LS because HKL s were not integers within tolerance i Cancel Figure 4 38 3 reflections removed from LS 4 15 Data Collection 3 Press OK SMART displays Least Squares Output window showing among other data a histogram for the refl
48. o and 0 0334 for all 2435 data wR 0 0673 GooF 5 O 675 Restrained GooF U 575 for all data R1 0 0325 for 1436 unique reflections after merging for Fourier Highest peak 0 29 at 0 6214 0 4402 0 1532 0 72 A from C1 Deepest hole 0 17 at 01898 0 4771 0 0215 1 28 A from TTE sis mis mis sis ee eee ee ee RR Y LIDim finished at 17 01 09 Total elapsed time 3 6 Secs ais mis mis sis sis mis mis sis sis mbs sis mis mis mia mia mi mi da mi sis mis mi ia mis is mis mis mis mi sis sis mis sis mis mis mis mbs mis mis mis ia mi mi mi ia mi mis mi is mis mis mbs mis mis mis mi mis is mis mia is mis mis sis mia mis mi mia mia mis mia ia mia aia mia mia a Figure 6 37 Refinement control Note that the suggested weighting scheme has values of 0 0485 and 0 000 You are now ready for the final least squares refinement run 6 28 M86 E04015 1001 SMART APEX User s Manual Structure Determination amp Refinement 45 Check the Acta box to create cif files for publication Click OK to launch the XL least squares refinement program Figure 6 38 Mean shifl ezd 0566 Maximum 4 142 for OSF at 17 09 07 Max shift 0 007 A for H10C Max dU 0 001 for C10 wR 010778 before cycle 2for 2435 data and 130 130 parameters GooF 5 1 029 Restrained GooF 1 029 for 0 restraints Mean shifl ezd 0 226 Maximum 3 951 for EXTI at 17 09 08 Max shift 0 002 for H10C Max dU 0 000 for C10 WR O 0776 before cycle 3
49. ogram has created YLID1m ins file and an YLID1m hkl file recall Figure 6 1 You are now ready to solve the structure of the YLID sample 19 Click on the XS command at the top of the menu to launch the XS structure solution program Figure 6 18 C NWINNTNSystem32NCMD exe Reflections and 1666 unique TPR for phase annealing Phases refined using 2642 unique TPR Reflections and 3344 unique TPR for R Calpha gt Unique negative quartets found 594 used for phase refinement Unique NQR employed in phase annealing Parallel refinements highest memory 4261 44577 Ralpha Nqual Sigma 1 lt lt CFOM Seminvariants 6 653 8 775 6 967 1 122 U 853 9111 6 3180000000000011000000108080 6 128 0 053 816 0 967 1 131 8 80853 20719 9400000000100111000001U080 80 6 256 256 Phase sets refined best is code 181393 with CFOM 6 6529 Fourier and peaksearch RE 8 138 for 14 atoms and 452 E values Fourier and peaksearch RE 0 118 for 14 atoms and 452 E values Fourier and peaksearch Se ae ie eile aie ie eile aie oe ie eile oie ie eile oie ae ie oie GA G4 eile oi aie ie oie oe ie eile oie oe aie eile oi ie ie oie oie ie aie oe ie ie oie oie ie aie oi ae ie oie ae ie ie a ae ie ei oie ae ie ae oe ae ie ee ae ie ie B B Bb B ylidim finished at 07 57 27 Total elapsed time 4 1 secs SEE 4 4 4 4 4 4 4 4 4 d 4 B d B ttt Ht ttt tt
50. on matrix0 002 03 05 00 17 43 38 Created 03 0 23 696 Distance size Project v ir s ylid1l v d WorkDir s ylid1 2 Theta 23 40 Phi 0 00 Chi 54 80 Distance 5 984 FloodFld 4004L170 Spatial LINEAR Dar 4004L010 Size Spd 512 400 ollecting matrix0 003 Disk Kb 1578112 Time used left 0 00 29 0 14 11 Figure 4 31 Frame collection MATRIXO MATRIX1 and MATRIX2 When all frames have been collected SMART performs the steps of thresholding indexing Bravais lattice determination and least squares refinement of cell constants The YLID test crystal has an orthorhombic primitive unit cell as shown in Figure 4 32 M86 E04015 1001 SMART APEX User s Manual Data Collection Least Squares Output Figure 4 32 Least squares output The YLID test crystal should have an orthorhombic Primitive cell with approximate cell dimensions of a 5 95A b 9 03A c 18 38A and 90 You are now ready to collect data M86 E04015 1001 4 13 Data Collection 45 Data Collection Perform data collection as follows 1 From the SMART program click Acquire Hemisphere SMART displays the data collection options Figure 4 33 SCAN HEMISPHERE Options x Job name YLID1 Title YLID Test Crystal Max display counts 1 Suppress correlation Y7N Check for yes Suppress bias detn Y N Check for yes XENGEN output format Checkfor yes Sequence of starting run 1 Sequence of end
51. on amp Refinement 5 The lattice is Primitive P Press RETURN The second XPREP window appears Figure 6 6 BIGXPREP V5 1 Copyright 1997 Bruker AXS Current dataset ylidim rav Original cell 5 960 9 034 18 384 90 0 Esds 0 000 0 001 0 001 30 Current cell 5 960 9 03 8 38 90 00 Matrix 1 0000 0 0000 0 0000 0 0000 1 0000 Read modify or merge DATASETS Contour PATTERSON sections search for HIGHER metric symmetry 5 Determine or input SPACE GROUP 4 Apply ABSORPTION corrections L Reset LATTICE type of original cell Select option H Figure 6 6 Second XPREP window 6 4 Wavelength 0 71073 Chiral 90 00 90 00 0 00 0 00 90 00 90 00 Vol 0000 0000 0 0000 1 0000 Define unit cell CONTENTS Set up shelxtl FILES RECIPROCAL space displays UNIT CELL transformations Change TOLERANCES QUIT program SMART APEX User s Manual M86 E04015 1001 SMART APEX User s Manual Structure Determination amp Refinement 6 Press RETURN to execute the search for higher metric symmetry H The program has determined that the YLID crystal has an orthorhombic primitive lattice Figure 6 7 BIGXPREP V5 1 Copyright 1997 Bruker AXS Current dataset ylidim raw Wavelength 0 71073 Chiral Original cell 5 960 9 034 8 38 90 00 90 00 90 00 Esds 0 001 current cell Matrix 1 0000 0 0000 0000 0000 1 0000 0 0000 0 0000 1 0000 Read modify or merge DATASETS Define unit
52. process Click on a p p or frame filename with the base name of the series of frames you wish to process Look in f E3 Files of type files Cancel Frames path E frames Output directory C frames Vlid work Figure 5 3 Select a P4P file A summary window appears showing the name and directories used by the project Figure 5 4 SMART APEX User s Manual Project SAINT SADABS XPREP Utility Edit Name ylid Crystal Type Small Molecule Frames Directory Path C frames Ylid ylid Output Directory CAframesYYlidyworky Figure 5 4 SAINT project summary window 5 Click SAINT gt Initialize to initialize the project 6 Click SAINT gt Execute An input box appears summarizing the information that SAINT has determined Figure 5 5 M86 E04015 1001 SMART APEX User s Manual Data Integration Basic SAINT menu for analyzing small molecule area detector frames 1 X Title Integrate Laue class mmm orthorhombic a b c 90 90 90 Js Lattice centering primitive Sort Cell parameters Global A 5 3551 Resolution limit for output theta degrees gin theta lambda 1 angstroms 0 790000 d spacing angstroms 83 335 Filter B 9 0322 09 91 Instrument E 18 3 44 30 011 Integration files Maximum wait for frame file seconds 0 000000 Starting Frame Filename H of Frames
53. scan absorption corr Copy file TRANSFORM hkl and cosines MAD S45 SIR or SIRAS pply HIGH low resolution cutoffs N NORMALIZE scale sigmas EXIT to main menu 0 QUIT program t select option 5 Figure 6 11 Next XPREP window 6 8 M86 E04015 1001 SMART APEX User s Manual Structure Determination amp Refinement 11 Press RETURN to choose the display intensity statistics option S The next XPREP window appears Figure 6 12 ver 6 07 Win Copyright Bruker AXS 2000 Current dataset ylidim hk ts not Friedel opposites A alents including Friedel opposites merge datasets menu QUIT progratr ect option Figure 6 12 Next XPREP window 12 Press RETURN to choose the merge all equivalents including Friedel mates option A The next XPREP window appears Figure 6 13 Compare data in the circled areas and note that the data set is virtually complete to 0 75 with an average redundancy of gt 4 The overall Rmerge iS 2 72 XPREP ver 6 07 Win Copyright Bruker AXS 2000 Resolution Data Theory Complete Redundancy Mean Mean I s Rint Rsiqma 0 0054 0 0078 0 0101 0 0140 0 0170 se au 70 45 30 LS 25 4 99 2 100 0 100 0 100 0 100 0 100 0 100 0 100 0 x O Cn Cn cy Gn n 7 e REN 100 0 d c 99 7 4 70 d b x 2 Merged A lowest resolution 18 36 Angstroms 357 outliers
54. so most of the information in the current SMART SAINT and ASTRO manuals applies to the SMART APEX system and the other SMART CCD systems From a hardware viewpoint the SMART APEX also shares common hardware components Other members of this new generation of instruments include the D8 ADVANCE and D8 DISCOVER and the D8 GADDS systems for general diffraction Documentation on some of these common hardware and software components is M86 E04015 1001 available in the user s manuals for the D8 family of instruments 1 2 How to Use This Manual This manual covers basic tutorial steps to get you started using the SMART APEX X ray diffractometer system The manual leads you step by step through an actual data collection and structure determination experiment performed on a typical system Additional reference is made where necessary to related program manuals SMART SAINT ASTRO and SHELXTL appendices other factory documentation and standard crystallographic reference materials And special notes are included where new users tend to have problems Information is organized in this manual as follows e Section 1 Introduction presents system features and instructions on using this manual e Section 2 Software Overview provides details on the software used with the system Introduction Section 3 Hardware Overview provides details on the system configuration for those not familiar with the equipment Includ
55. t ylidim rav 5 960 9 034 18 464 0 001 0 001 90 00 90 00 90 00 Original cell Esds 2 000 0 00 0 00 Current cell 90 00 90 00 Matrix 1 0000 19 Crystal system Orthorhombic Formula 4 00 C11 H10 O2 S Density 1 384 7 7 32 00 D Read modify or merge DATASETS P Contour PATTERSON sections H Search for HIGHER metric symmetry 5 Determine or input SPACE GROUP 4 Apply ABSORPTION corrections L Reset LATTICE type of original cell QUIT program select option F Output file name without extension YLID ir File ylidim ins set up as follows TITL YLIDim in 2 1 2 1 2 1 CELL 0 71073 ZERR 4 00 LATT 1 SYMM 0 5 Y SYMM 0 5 Y 0 5 7 SYMM 5 0 5 Z SFAC C HOS UNIT 44 40 6 4 TEMP 23 TREF HELF 4 END Do you wish to over write the intensity data file Figure 6 17 Next window M86 E04015 1001 Wavelength 0 710 chi Define unit cell Set up shelxtl FILES RECIPROCAL space UNIT CELL transformations Change TOLERANCES vlidim hkl Structure Determination amp Refinement 17 Press RETURN to keep the current name then type Y to write the YLID1m HKL file 18 You may now press RETURN for option E to return to the main SHELXTL menu 73 Errem 989 6 Lattice P 1 0000 Laue Formula wt Mu mm i1 CONTENTS displays N 6 13 Structure Determination amp Refinement The XPREP pr
56. t ttt BB BGB GB ttt ttt ttt ttt tt tt Press any key to continue Figure 6 18 Launch the XS program 20 When the program has finished running press RETURN The SHELXTL summary window redisplays recall Figure 6 3 6 14 SMART APEX User s Manual M86 E04015 1001 SMART APEX User s Manual Structure Determination amp Refinement 21 Click on the XSHELL button to start the XSHELL program The Fourier peaks will be displayed Figure 6 19 UNT File Edit Refine Select Atoms View Preferences Labels Fender Help Figure 6 19 Fourier peaks M86 E04015 1001 6 15 Structure Determination amp Refinement SMART APEX User s Manual 22 You may rotate the structure by dragging Note You can also use the S key to the mouse with the left button depressed select a peak directly Select all false peaks peaks Q14 to Q22 in the example shown by moving the The peak should turn blue when selected mouse to each peak and clicking the right The molecule may be rotated during this mouse button process Figure 6 20 Note For more detailed instructions on use of the XSHELL program see the XSHELL User s Manual File Edit Refine Select Atoms View Preferences Labels Render Figure 6 20 Molecule with peaks Q14 to Q22 selected 6 16 M86 E04015 1001 SMART APEX User s Manual Structure Determination amp Refinement 23 When all false peaks have been selected 24 Select the 11 peaks that correspond to click th
57. the El button A periodic table will appear Figure 6 25 VIIA He VIA VIIA Li B C N 0 ne Na a IB K ca se w ou zn Ge as se Rb Sr Y Z Nb Ru Cd In Sn Sb Xe Cs La W Re Os Ir Pt Hg TI Bi Rn Pr Nd Sm Eu Gd Tb Dy Er Tm Yb Lu Cancel feed ol LL els fo Lol Figure 6 25 Periodic table M86 E04015 1001 SMART APEX User s Manual Structure Determination amp Refinement 28 Click the O button for Oxygen A panel appears for you to label these peaks Figure 6 26 ylid1 m res Jof x File Edit Refine Select Atoms View Preferences Labels Render Cancel Note Leave empty any field which you do not wish changed Also the program will Help Initial Number Order Ascending C Descending truncate any label over Trailer 4 characters long Figure 6 26 Input panel appears 29 Click OK to label the peaks as O with a 3j Extinction mel oz starting number of 1 Anisol nwet Fourier Diference Map eres j 30 Click the Refine button at the top of the m XSHELL Menu A panel will appear mex Figure 6 27 Sugesed BEEN BEEN m Progr
58. ts averaged 11 Averaged orientation UB matrix 0 1131002 0 0218930 0 038905 0 0016071 0 1067129 0 0149832 0 1245288 0 0212608 0 035141 eighted average cell constants B C Alpha Beta Gamma vol 5 9440 3 0100 18 3419 90 000 90 000 90 000 982 31 0 0004 0 0006 0 0015 0 003 0 003 0 002 0 20 Std deviations of the 11 input local LS results 0 0059 0 0027 0 0184 0 000 0 000 0 000 1 58 Range of reflections used 4 4 2 Figure 5 10 Viewing log files Your results should be similar to those displayed above 13 Press Enter and close all SAINT windows and exit from the SAINT menu You are now ready to begin the structure determination and refinement process M86 E04015 1001 5 7 Data Integration 5 8 SMART APEX User s Manual M86 E04015 1001 6 Structure Determination amp Refinement You are now ready to solve and refine the crystal structure for the YLID test crystal The integration process SAINT has produced two important files YLID1M p4p containing the final unit cell parameters and other important information on how the experiment was carried out and YLID1M raw containing the actual intensity data These files are all that is SAINT name p4p name RAW XPREP name INS name HKL m gt XS Cycle until good trial name RES solution found XSHELL 5 gt XL Cycle unti
59. tter and a graphite crystal monochromator The sealed tube X ray source with a molybdenum Mo target produces the X ray beam used by the SMART APEX 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 71073A emitted from the Mo X ray source and passes it down the collimator system SMART Rotary Shutter and Collimator The monochromatic X ray beam then passes through the labyrinth the SMART rotary shutter and the incident beam collimator before striking the specimen e he labyrinth is a spring loaded device which ensures that the collimator and the SMART shutter are tightly connected to prevent X ray leakage e The SMART shutter is a device which precisely controls the exposure time for each frame during data collection Its M86 E04015 1001 SMART APEX User s Manual status lamps indicate when the shutter is open ON and closed OFF This assembly also houses an automatic attenuator e The incident collimator is equipped with pinholes at both front near crystal and rear near source These pinholes help to define the size and shape of the incident X ray
60. y the summary table from the integration process Figure 5 2 C SAXINSAINT 32 SAINT_exe lal x 24 000 0 0 0 000 0 00 0 00 0 000 0 000 0 0 0 000 0 000 0 00 00 OO OO 00l 25 000 Overall Pairs Unig Merg lt 25 I lt 519 gt Bg Rsym dI I dI s R Ranom Canom ErX ErY Erz 0 000 7061 1279 1454 7027 9 1 1704 109 35 81 2 49 0 027 0 000 0 7 0 025 0 026 0 82 01 02 02 24 1 000 Centric Pairs Unig Merg lt 25 I lt 519 gt Bg Rsym dI I dI s R Ranom Canom ErX ErY Erz 0 000 1268 280 452 1235 16 5 2508 639 49 56 2 57 0 022 0 000 0 7 0 018 0 029 1 15 03 02 01 25 1 000 overage Statistics Shell Angstrms 065 Theory SComp Redund Rsym Pairs amp Pairs Rshell lt 25 to 1 616 176 178 98 88 5 65 0 020 149 83 71 0 020 97 04 3 5 to 1 283 325 328 99 09 5 88 0 022 282 85 98 0 027 38 46 1 9 to 1 120 471 476 98 95 5 79 0 023 412 86 55 0 037 26 5 3 7 to 1 018 612 618 99 03 5 67 0 024 538 87 06 0 037 17 22 6 6 to 0 945 762 765 99 61 5 49 0 025 668 87 32 0 040 13 52 7 0 to 0 889 901 906 99 45 5 35 0 025 792 87 42 0 047 10 32 11 8 to 0 845 1035 1040 99 52 5 22 0 026 913 87 79 0 055 7 72 11 0 to 0 808 1185 1189 99 66 5 09 0 026 1045 87 89 0 059 6 89 16 2 to 0 777 1318 1323 99 62 4 98 0 026 1164 87 98 0 070 5 70 23 3 to 0 750 1454 1454 100 00 4 86 0 027 1279 87 96 0 082 4 75 19 4 Averaged local cell least squares refinement 08 08 00 13 48 17 Number of local refinemen

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