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Processing OX2R data (5WQC)

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keitaroyam edited this page Jan 23, 2018 · 14 revisions

The following describes how OX2R datasets can be processed using KAMO (documentation in Japanese / English).

References

  • Original paper
    • Suno et al. (2017) "Crystal Structures of Human Orexin 2 Receptor Bound to the Subtype-Selective Antagonist EMPA." Structure doi: 10.1016/j.str.2017.11.005 PDB: 5WQC

Raw data

  • Available in Zenodo. DOI
  • Collected on BL32XU, SPring-8
  • MX225HS CCD detector (2x2 binning), 1 Å wavelength
  • Manually collected data
    • 466 datasets (but one lost) from 36 pins
    • 10×8 μm2 beam
    • 1, 2, 3, 4, or 6°/dataset (mostly 3°), mostly 1°/frame (2°/frame when 2°/dataset), shuttered collection
  • Automatically collected data (ZOO)
    • 339 datasets from 26 pins
    • Mostly 10×8 μm2 beam (one 5×5, twenty 15×8 μm2 datasets)
    • 5 or 6°/dataset, 1°/frame, shuttered collection (without 4 shutterless datasets)
  • C2; a=94.13, b=75.52, c=95.93 Å, β=111.39°

How data were processed in the original paper

As this was the first sample for small-wedge data collection at BL32XU, various data collections parameters were tested. In original paper, they were all processed and merged (outliers were rejected).

The current version of KAMO skips datasets consisting of single frames. Here 28 single-frame datasets (2°/frame) are included. Unfortunately it is not straightforward to reproduce the original result using current KAMO.

XDS ver. March 1, 2015 was used for processing individual wedges (indexing and integration). In merging XSCALE ver. Jun 17, 2015 (BUILT=20150617) was used.

768 datasets were indexed and integrated with the consistent unit cell. Then kamo.multi_merge was used at 1.90 Å, but finally-selected datasets (in run_03/ of the largest cluster) were re-scaled at 1.96 Å. Following is the final statistics with 631 datasets:

 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  CC(1/2)  Anomal  SigAno   Nano
   LIMIT     OBSERVED  UNIQUE  POSSIBLE     OF DATA   observed  expected                                      Corr

     5.87       81602    1739      1753       99.2%       9.3%     10.4%    81600   49.64      9.4%    99.9*    13*   0.924    1551
     4.15      150700    3115      3120       99.8%      13.4%     11.9%   150700   43.52     13.5%    99.9*     7    1.013    2921
     3.39      192982    3974      3979       99.9%      18.2%     16.0%   192982   31.84     18.4%    99.8*     6    0.988    3788
     2.94      225526    4648      4654       99.9%      30.8%     31.5%   225526   18.46     31.1%    99.5*     3    0.821    4455
     2.63      255918    5277      5280       99.9%      50.3%     54.0%   255918   12.05     50.8%    99.3*     4    0.775    5088
     2.40      283459    5869      5878       99.8%      89.6%     99.9%   283459    7.44     90.5%    98.0*     1    0.715    5676
     2.22      308888    6421      6427       99.9%     144.9%    165.3%   308888    4.86    146.5%    95.8*     1    0.676    6224
     2.08      316963    6632      6635      100.0%     244.0%    285.4%   316963    3.07    246.6%    90.9*     1    0.642    6447
     1.96      335800    7339      7344       99.9%     510.2%    619.4%   335800    1.68    515.8%    78.3*    -3    0.584    7158
    total     2151838   45014     45070       99.9%      39.3%     42.7%  2151836   13.45     39.7%    99.8*     2    0.746   43308
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