8. Examine Data
kpa
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.
8.1XPREP
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.
Figure 8.1 - Select files for XPREP input
NOTE: In this example, the scaling process has created two files: ylid_manual_0m.p4p contain-ing the final unit cell parameters from integration and ylid_manual_0m.hkl containing the cor-rected intensities. Typically, these are the files to use for determining space groups, but you can browse to choose other files.
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8.2Space 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.
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<b<c), the original and reduced cells are the same (see Figure 8.3). Press Enter to search for a higher symmetry cell.
Figure 8.3 - Reduced cell
For the YLID, no higher symmetry cell is found. The program has determined that the YLID crys-tal has an orthorhombic primitive lattice (see
Figure 8.4). Press Enter to accept.
Figure 8.4 - Higher symmetry cells
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3.The next logical step is to determine the
space group. XPREP suggests this (see Figure 8.5). Press Enter to determine the
space group.
Figure 8.5 - Determine the space group
4.If the space group is known or if the com-pound is known to be chiral, enter that infor-mation (see Figure 8.6). Generally, it is sufficient to press Enter to start the space
甲壳素group determination.
Figure 8.6 - Space Group options
5.XPREP has chosen the crystal system [O]
(see Figure 8.7). Press Enter to accept.甘远志
Figure 8.7 - Choose the crystal system
6.XPREP has chosen the crystal lattice [P]回馈单元 (see Figure 8.8). Press Enter to accept.
Figure 8.8 - Choose the lattice
7.XPREP evaluates the data and looks at the
systematic absences for all possible glide planes and screw axes (see Figure 8.9). These are displayed across the middle of the figure. By examining the number of reflections with I>3 sigma(I), 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.
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8.3Reflection 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 data set. Press Enter to accept.2.There are multiple choices for data manipu-lation (see Figure 8.10). “S” chooses a dis-
play of statistics.
Figure 8.10 - The data manipulation menu
3.The data can be merged in several ways.
Choose the “Merge ALL equivalents includ-ing Friedel opposites” option [A] (see Figure 8.11). Press Enter to accept.NOTE : This merge will not average the reflec-tions in the final data file. It is only for the calcu-
lation of statistics.
Figure 8.11 - The merge data menu
4. A table of statistics appears (see Figure
8.12). Examine the data presented. Is 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 compare all of the data with the high-resolu-tion 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 I/sigma(I) will usually be quite different. The Mean I/sigma(I) for the high-resolution data should be greater than 3.0.
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For this data set, when integrated to 0.67Å reso-lution, the difference between the Rint for the high-resolution data and the complete data set is slightly larger than expected. Press Enter to
continue.
Figure 8.12 - Intensity statistics
8.4Applying High Resolution Cutoff
NOTE : For the YLID crystal, if the resolution limit for integration was changed to 0.75 as sug-gested on Page 7-3, then there will be no need to apply a High Resolution Cutoff at this point.
1.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.
行学一族Figure 8.13 - Requesting a high resolution cutoff 2.Enter a high resolution limit of 0.75 (see Fig-ure 8.14) and press Enter to accept the low
resolution cutoff of infinity.
Figure 8.14 - The resolution cutoff menu
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