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Processing BLT1 data (5X33)

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keitaroyam edited this page Jan 23, 2018 · 2 revisions

The following describes how BLT1 datasets can be processed using KAMO (documentation in Japanese / English).

References

  • Original paper
    • Hori et al. (2018) "Na+-mimicking ligands stabilize the inactive state of leukotriene B4 receptor BLT1." Nature Chemical Biology doi: 10.1038/nchembio.2547 PDB: 5X33

Raw data

  • Available in Zenodo. DOI
  • Collected on BL32XU, SPring-8
  • EIGER X 9M, 5×5 μm2 beam, 1 Å wavelength
  • 2.5°/dataset, 0.5°/frame (shutterless)
  • 1296 datasets collected manually from 14 cryoloops
  • P22121; a=69.6, b=77.6, c=135.5 Å

How data were processed in the original paper

GUI command 'kamo' was used by default parameters. XDS (ver. May 1, 2016 BUILT=20160617) was used for integration and no prior crystal information was employed.

In the published result, it seems that only pin numbers 1-10 were processed and merged (before KAMO processed all datasets). 623 out of 1139 datasets were indexed and integrated, and 559 datasets belonged to the largest group of consistent unit cells:

   freq symmetry     a      b      c     alpha  beta   gamma reindex
    480 P 1         69.57  77.63 135.52  90.75  90.88  90.46 a,b,c
     25 P 1 2 1     69.57  77.63 135.52  90.75  90.88  90.46 a,b,c
     22 P 1 2 1     69.57 135.52  77.63  89.25  90.46  89.12 a,-c,b
     22 P 1 2 1     77.63  69.57 135.52  89.12  90.75  89.54 b,-a,c
      1 C 1 2 1    104.65 103.82 135.52  91.15  90.03  96.27 a-b,a+b,c
      1 C 1 2 1    103.82 104.65 135.52  89.97  91.15  83.73 a+b,-a+b,c
      8 P 2 2 2     69.57  77.63 135.52  90.75  90.88  90.46 a,b,c
      0 C 2 2 2    103.82 104.65 135.52  89.97  91.15  83.73 a+b,-a+b,c
      0 P 4         69.57  77.63 135.52  90.75  90.88  90.46 a,b,c
      0 P 4 2 2     69.57  77.63 135.52  90.75  90.88  90.46 a,b,c

P222 symmetry was selected, but its frequency was so small probably due to small reciprocal space coverage (2.5°/crystal).

Finally, clustering by BLEND was executed, but the largest cluster was taken. This result consisted of 494 datasets and was found in blend_3.7A_framecc_b/cluster_0558/run_03/XSCALE.LP:

 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

    11.04       12009     365       375       97.3%      15.9%     13.8%    12009   31.94     16.2%    99.9*     4    1.064     210
     7.83       21128     593       593      100.0%      20.8%     17.6%    21128   24.84     21.0%    99.5*     6    1.073     437
     6.40       22557     745       745      100.0%      47.2%     48.0%    22557    9.71     48.0%    97.8*     3    0.890     582
     5.55       29137     862       862      100.0%      94.7%    106.1%    29136    5.31     96.2%    95.2*     5    0.817     700
     4.96       35154     984       984      100.0%     115.0%    127.9%    35154    4.96    116.7%    92.9*    -2    0.794     822
     4.53       38603    1060      1060      100.0%     148.8%    161.8%    38603    4.39    150.9%    91.7*     2    0.837     898
     4.19       42878    1170      1170      100.0%     187.0%    211.0%    42878    3.41    189.6%    84.3*    -3    0.776    1006
     3.92       45019    1244      1244      100.0%     388.7%    466.8%    45019    2.01    394.1%    70.3*     1    0.683    1087
     3.70       40261    1268      1268      100.0%     733.9%    908.3%    40261    1.09    745.7%    53.5*     0    0.632    1107
    total      286746    8291      8301       99.9%     155.8%    180.6%   286745    6.71    158.1%    95.7*     1    0.790    6849

This result was produced by the following command:

#!/bin/sh
# settings
dmin=3.7 # resolution
anomalous=false # true or false
lstin=formerge.lst # list of XDS_ASCII.HKL files
use_ramdisk=true # set false if there is few memory or few space in /tmp
# _______/setting

kamo.multi_merge \
        workdir=blend_${dmin}A_framecc_b \
        lstin=${lstin} d_min=${dmin} anomalous=${anomalous} \
        program=xscale xscale.reference=bmin \
        reject_method=framecc+lpstats rejection.lpstats.stats=em.b \
        clustering=blend blend.min_cmpl=90 blend.min_redun=4 blend.max_LCV=None blend.max_aLCV=None \
        xscale.use_tmpdir_if_available=${use_ramdisk} \
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