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JOBS= INTEGRATE CORRECT | JOBS= INTEGRATE CORRECT | ||
Afterwards, another xds_par run gives the final intensities. Repeating this optimization sometimes helps. | Afterwards, another xds_par run gives the final intensities. Repeating this optimization sometimes helps. | ||
=== Peak === | === Peak === | ||
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NUMBER OF UNIQUE ACCEPTED REFLECTIONS 159845 | NUMBER OF UNIQUE ACCEPTED REFLECTIONS 159845 | ||
The verdict is clear: bad ISa, anomalous correlation > 30% only to about 5 A. The reason becomes clear if we load FRAME.cbf into [[XDS-Viewer]], and zoom in: | The verdict is clear: high mosaicity (> 0.5°) bad ISa, anomalous correlation > 30% only to about 5 A. The reason becomes clear if we load FRAME.cbf into [[XDS-Viewer]], and zoom in: | ||
[[File:3csl-frame.png]] | [[File:3csl-frame.png]] | ||
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R_d helps to quantify radiation damage. Unfortunately, for this dataset this "R-factor as a function of frame number difference" behaves wildly, so we cannot use 0-dose extrapolation, like we successfully did for [[1Y13]]. | R_d helps to quantify radiation damage. Unfortunately, for this dataset this "R-factor as a function of frame number difference" behaves wildly, so we cannot use 0-dose extrapolation, like we successfully did for [[1Y13]]. | ||
=== High-remote === | |||
Due to a beamline problem, high-remote data collection stopped after 269 frames of 0.5° (the final frame is already affected). After restart of the beamline, another 100 frames were collected but they later turned out to merge badly with the first 269 frames - a hint that the monochromator was still heating up, or similar. So the latter frames were left out. The 269 frames are [ftp://turn5.biologie.uni-konstanz.de/pub/datasets/3csl-hrem.tar here] (1.4 Gb). | |||
From CORRECT.LP : | |||
a b ISa | |||
6.595E+00 3.032E-04 22.36 | |||
... | |||
NOTE: Friedel pairs are treated as different reflections. | |||
SUBSET OF INTENSITY DATA WITH SIGNAL/NOISE >= -3.0 AS FUNCTION OF RESOLUTION | |||
RESOLUTION NUMBER OF REFLECTIONS COMPLETENESS R-FACTOR R-FACTOR COMPARED I/SIGMA R-meas Rmrgd-F Anomal SigAno Nano | |||
LIMIT OBSERVED UNIQUE POSSIBLE OF DATA observed expected Corr | |||
8.21 20187 6913 7245 95.4% 2.9% 3.3% 20065 27.89 3.6% 2.9% 63% 1.625 3050 | |||
5.84 36272 12417 12782 97.1% 5.5% 5.3% 36116 17.46 6.8% 7.0% 33% 1.196 5727 | |||
4.78 46716 16015 16500 97.1% 6.8% 6.5% 46473 14.43 8.4% 10.0% 19% 1.004 7416 | |||
4.15 55299 18949 19484 97.3% 7.5% 7.2% 55003 13.00 9.3% 11.7% 10% 0.896 8818 | |||
3.71 63751 21798 22065 98.8% 12.2% 12.2% 63371 8.51 15.1% 20.2% 6% 0.819 10225 | |||
3.39 70787 24180 24422 99.0% 19.5% 20.0% 70378 5.58 24.0% 33.3% 5% 0.786 11343 | |||
3.14 61197 25100 26452 94.9% 32.5% 34.2% 57925 2.88 41.3% 63.9% 4% 0.740 9652 | |||
2.94 40481 21869 28566 76.6% 53.5% 57.8% 33568 1.42 72.1% 112.8% -2% 0.663 6208 | |||
2.77 24584 16962 30228 56.1% 76.4% 82.4% 15055 0.77 107.5% 163.0% 2% 0.660 2828 | |||
total 419274 164203 187744 87.5% 10.3% 10.4% 397954 8.06 12.9% 24.7% 14% 0.882 65267 | |||
NUMBER OF REFLECTIONS IN SELECTED SUBSET OF IMAGES 428770 | |||
NUMBER OF REJECTED MISFITS 9102 | |||
NUMBER OF SYSTEMATIC ABSENT REFLECTIONS 0 | |||
NUMBER OF ACCEPTED OBSERVATIONS 419668 | |||
NUMBER OF UNIQUE ACCEPTED REFLECTIONS 164343 | |||
=== Inflection === | === Inflection === | ||
| Line 184: | Line 183: | ||
NUMBER OF ACCEPTED OBSERVATIONS 528412 | NUMBER OF ACCEPTED OBSERVATIONS 528412 | ||
NUMBER OF UNIQUE ACCEPTED REFLECTIONS 166224 | NUMBER OF UNIQUE ACCEPTED REFLECTIONS 166224 | ||
== Scaling == | |||
== Structure solution == | |||
We use [[ccp4com:hkl2map|hkl2map]] for solving the structure. | |||
=== [[ccp4com:SHELX C/D/E|SHELXC]] statistics === | |||
[[File:3csl-completeness.png]] | |||
[[File:3csl-chi2.png]] | |||
[[File:3csl-i-sigi.png]] | |||
[[File:3csl-anom.png]] | |||
[[File:3csl-d".png]] | |||
[[File:3csl-self-anom.png]] | |||
=== [[ccp4com:SHELX C/D/E|SHELXD]] statistics === | |||
[[File:3csl-ccall-ccweak-5A.png]] | |||
[[File:3csl-ccall-patfom-5A.png]] | |||
[[File:3csl-hist-5A.png]] | |||
[[File:3csl-occup-5A.png]] | |||
=== [[ccp4com:SHELX C/D/E|SHELXE]] statistics === | |||
Since there are 1852 residues in the ASU, the solvent content is about 72.5%. The correct hand ("inverted") becomes immediately clear - it is superior in all respects than the "original" hand. | |||
[[File:3csl-contrast.png]] | |||
[[File:3csl-connectivity.png]] | |||
[[File:3csl-ccmap.png]] | |||
Then we try to get a poly-ala backbone tracing: | |||
shelxe.beta -a -q -m15 -s0.725 -b -h16 -n2 -i mad mad_fa | |||