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3CSL (view source)

Revision as of 18:49, 18 March 2011

940 bytes added ,  18 March 2011
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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.
=== 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


=== 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 ===
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  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
Kay
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