1Y13

From XDSwiki

The structure is deposited in the PDB, solved with SAD and refined at a resolution of 2.2 A in spacegroup P4(3)2(1)2 (#96). The data for this project were provided by Jürgen Bosch (SGPP) and are linked to the ACA 2011 workshop website and here. There are two high-resolution (2 Å) datasets E1 (wavelength 0.9794Å) and E2 (@ 0.9174Å) collected (with 0.25° increments) at an ALS beamline on June 27, 2004, and a weaker dataset collected earlier at a SSRL beamline. We will only use the former two datasets here.

Dataset E1

Use generate_XDS.INP and run xds once. Based on R-factors in the resulting CORRECT.LP, and an inspection of BKGPIX.cbf, I modified XDS.INP to have

INCLUDE_RESOLUTION_RANGE=40 2.1                       ! too weak beyond 2.1 Å
VALUE_RANGE_FOR_TRUSTED_DETECTOR_PIXELS=8000. 30000.  ! raised from 7000 30000 to mask beamstop

and ran xds again.

What's the problem?

This is the excerpt from CORRECT.LP :

SPACE-GROUP         UNIT CELL CONSTANTS            UNIQUE   Rmeas  COMPARED  LATTICE-
  NUMBER      a      b      c   alpha beta gamma                            CHARACTER

      5     145.8  145.7  131.4  90.0  90.0  90.0    9735    24.5    23176    10 mC
     75     103.1  103.1  131.4  90.0  90.0  90.0    5262    23.4    27649    11 tP
     89     103.1  103.1  131.4  90.0  90.0  90.0    2911    22.8    30000    11 tP
     21     145.7  145.8  131.4  90.0  90.0  90.0    5270    23.2    27641    13 oC
      5     145.7  145.8  131.4  90.0  90.0  90.0    9681    24.2    23230    14 mC
      1     102.9  103.2  131.4  90.0  90.0  89.9   18040     6.9    14871    31 aP
  *  16     102.9  103.2  131.4  90.0  90.0  90.0    5568     9.1    27343    32 oP
      3     103.2  102.9  131.4  90.0  90.0  90.0   10536     9.5    22375    35 mP
      3     102.9  103.2  131.4  90.0  90.0  90.0   10496     8.3    22415    33 mP
      3     102.9  131.4  103.2  90.0  90.1  90.0    9770     7.3    23141    34 mP
      1     102.9  103.2  131.4  90.0  90.0  90.1   18040     6.9    14871    44 aP

...

REFINED PARAMETERS:  DISTANCE BEAM ORIENTATION CELL AXIS                   
USING  219412 INDEXED SPOTS
STANDARD DEVIATION OF SPOT    POSITION (PIXELS)     1.01
STANDARD DEVIATION OF SPINDLE POSITION (DEGREES)    0.11
CRYSTAL MOSAICITY (DEGREES)     0.191
DIRECT BEAM COORDINATES (REC. ANGSTROEM)  -0.004789  0.003758  1.021015
DETECTOR COORDINATES (PIXELS) OF DIRECT BEAM    1027.25   1064.20
DETECTOR ORIGIN (PIXELS) AT                     1036.84   1056.68
CRYSTAL TO DETECTOR DISTANCE (mm)       209.38
LAB COORDINATES OF DETECTOR X-AXIS  1.000000  0.000000  0.000000
LAB COORDINATES OF DETECTOR Y-AXIS  0.000000  1.000000  0.000000
LAB COORDINATES OF ROTATION AXIS  0.999997  0.000527  0.002187
COORDINATES OF UNIT CELL A-AXIS    21.922    52.895    85.337
COORDINATES OF UNIT CELL B-AXIS     3.771    87.158   -54.992
COORDINATES OF UNIT CELL C-AXIS  -128.130    18.914    21.191
REC. CELL PARAMETERS   0.009731  0.009697  0.007620  90.000  90.000  90.000
UNIT CELL PARAMETERS    102.766   103.125   131.241  90.000  90.000  90.000
E.S.D. OF CELL PARAMETERS  1.3E-01 8.6E-02 9.3E-02 0.0E+00 0.0E+00 0.0E+00
SPACE GROUP NUMBER     16

So CORRECT chooses an orthorhombic spacegroup.

The file continues:

...
     a        b          ISa
6.058E+00  3.027E-04   23.35

...

      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

    6.23       17389    5807      6045       96.1%       2.4%      2.8%    17277   35.83     3.0%     2.0%    66%   1.553    2434
    4.43       32116   10536     10787       97.7%       2.7%      3.0%    32057   33.78     3.3%     2.4%    55%   1.272    4762
    3.62       41900   13700     13961       98.1%       3.4%      3.4%    41793   27.98     4.1%     3.6%    38%   1.115    6295
    3.14       51146   16371     16513       99.1%       5.4%      5.3%    50967   18.89     6.6%     7.2%    20%   0.961    7625
    2.81       59159   18627     18675       99.7%      12.7%     13.2%    58877    9.82    15.4%    18.0%     8%   0.818    8716
    2.56       65525   20596     20651       99.7%      28.5%     30.2%    65130    5.19    34.5%    40.4%     3%   0.757    9629
    2.37       71579   22491     22533       99.8%      62.6%     67.1%    71068    2.60    75.6%    88.8%     1%   0.694   10498
    2.22       74065   23837     24094       98.9%      97.9%     97.0%    73444    1.59   118.8%   139.8%    11%   0.738   11051
    2.09       65776   24379     25674       95.0%     133.3%    140.6%    63647    0.90   166.4%   216.0%     1%   0.651   10380
   total      478655  156344    158933       98.4%       6.5%      6.8%   474260   10.65     7.9%    22.5%    16%   0.852   71390


NUMBER OF REFLECTIONS IN SELECTED SUBSET OF IMAGES  492346
NUMBER OF REJECTED MISFITS                           13342
NUMBER OF SYSTEMATIC ABSENT REFLECTIONS                  0
NUMBER OF ACCEPTED OBSERVATIONS                     479004
NUMBER OF UNIQUE ACCEPTED REFLECTIONS               157108

Some comments:

  • the "STANDARD DEVIATION OF SPOT POSITION (PIXELS)" is significantly higher (1.01) than those reported for the 5°-batches in INTEGRATE.LP (about 0.6) . This suggests that the geometry refinement has to deal with inconsistent data.
  • CORRECT obviously indicates an orthorhombic spacegroup.
  • the number of MISFITS is higher than 1%. From the first long table (fine-grained in resolution) table in CORRECT.LP we learn that the misfits are due to faint high-resolution ice rings - so this is a problem intrinsic to the data, and not to their mode of processing.

To my surprise, pointless ("pointless xdsin XDS_ASCII.HKL") does not agree with CORRECT's standpoint:

Scores for each symmetry element
 
Nelmt  Lklhd  Z-cc    CC        N  Rmeas    Symmetry & operator (in Lattice Cell)

  1   0.959   9.91   0.99   65030  0.034     identity
  2   0.959   9.91   0.99  132222  0.035 *** 2-fold l ( 0 0 1)  {-h,-k,+l}
  3   0.958   9.87   0.99  110073  0.044 *** 2-fold h ( 1 0 0)  {+h,-k,-l}
  4   0.942   9.55   0.96  132646  0.109 *** 2-fold   ( 1 1 0)  {+k,+h,-l}
  5   0.958   9.87   0.99  111819  0.043 *** 2-fold k ( 0 1 0)  {-h,+k,-l}
  6   0.941   9.54   0.95  131842  0.109 *** 2-fold   ( 1-1 0)  {-k,-h,-l}
  7   0.937   9.50   0.95  224393  0.107 *** 4-fold l ( 0 0 1)  {-k,+h,+l} {+k,-h,+l}

and

    Laue Group        Lklhd   NetZc  Zc+   Zc-    CC    CC-  Rmeas   R-  Delta ReindexOperator

> 1  P 4/m m m  ***  1.000   9.73  9.73  0.00   0.97  0.00   0.07  0.00   0.2 [h,k,l]
- 2    P m m m       0.000   0.35  9.88  9.53   0.99  0.95   0.04  0.11   0.0 [h,k,l]
  3    C m m m       0.000  -0.02  9.72  9.74   0.97  0.97   0.07  0.07   0.2 [h+k,-h+k,l]
  4      P 4/m       0.000   0.07  9.77  9.70   0.98  0.97   0.06  0.08   0.2 [h,k,l]
  5  P 1 2/m 1       0.000   0.25  9.91  9.66   0.99  0.97   0.03  0.08   0.0 [-h,-l,-k]
  6  P 1 2/m 1       0.000   0.22  9.89  9.67   0.99  0.97   0.04  0.08   0.0 [h,k,l]
  7  P 1 2/m 1       0.000   0.21  9.88  9.67   0.99  0.97   0.04  0.08   0.0 [-k,-h,-l]
  8  C 1 2/m 1       0.000  -0.01  9.72  9.73   0.97  0.97   0.07  0.07   0.2 [h-k,h+k,l]
  9  C 1 2/m 1       0.000  -0.02  9.71  9.73   0.97  0.97   0.07  0.07   0.2 [h+k,-h+k,l]
 10       P -1       0.000   0.21  9.91  9.70   0.99  0.97   0.03  0.08   0.0 [h,k,l]

and

   Spacegroup         TotProb SysAbsProb     Reindex         Conditions
 
   <P 41 21 2> ( 92)    0.823  0.823                         00l: l=4n, h00: h=2n (zones 1,2)
   <P 43 21 2> ( 96)    0.823  0.823                         00l: l=4n, h00: h=2n (zones 1,2)
    ..........
    <P 4 21 2> ( 90)    0.095  0.095                         h00: h=2n (zone 2)
    ..........
   <P 42 21 2> ( 94)    0.077  0.077                         00l: l=2n, h00: h=2n (zones 1,2)

Thus suggesting #92 or #96 - the latter of which agrees with the PDB deposition. However, running CORRECT in #96 and specifying 103 103 130 90 90 90 as cell parameters, we obtain:

REFINED PARAMETERS:  DISTANCE BEAM ORIENTATION CELL AXIS                   
USING  220320 INDEXED SPOTS
STANDARD DEVIATION OF SPOT    POSITION (PIXELS)     1.17
STANDARD DEVIATION OF SPINDLE POSITION (DEGREES)    0.14
CRYSTAL MOSAICITY (DEGREES)     0.191
DIRECT BEAM COORDINATES (REC. ANGSTROEM)  -0.004790  0.004009  1.021014
DETECTOR COORDINATES (PIXELS) OF DIRECT BEAM    1027.19   1064.23
DETECTOR ORIGIN (PIXELS) AT                     1036.79   1056.20
CRYSTAL TO DETECTOR DISTANCE (mm)       209.52
LAB COORDINATES OF DETECTOR X-AXIS  1.000000  0.000000  0.000000
LAB COORDINATES OF DETECTOR Y-AXIS  0.000000  1.000000  0.000000
LAB COORDINATES OF ROTATION AXIS  0.999996  0.000901  0.002534
COORDINATES OF UNIT CELL A-AXIS    21.926    53.087    85.553
COORDINATES OF UNIT CELL B-AXIS     3.794    87.060   -54.995
COORDINATES OF UNIT CELL C-AXIS  -128.212    18.926    21.115
REC. CELL PARAMETERS   0.009704  0.009704  0.007616  90.000  90.000  90.000
UNIT CELL PARAMETERS    103.045   103.045   131.310  90.000  90.000  90.000
E.S.D. OF CELL PARAMETERS  2.1E-01 2.1E-01 2.1E-01 0.0E+00 0.0E+00 0.0E+00
SPACE GROUP NUMBER     96

...

    a        b          ISa
7.890E+00  8.793E-04   12.01

...

     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

    6.23       16770    2983      3017       98.9%       5.2%      6.1%    16752   26.20     5.7%     2.6%    55%   1.247    1223
    4.43       30598    5392      5393      100.0%       5.8%      6.2%    30596   25.25     6.3%     3.0%    50%   1.072    2420
    3.62       39822    6992      6994      100.0%       6.9%      6.6%    39820   22.27     7.6%     4.0%    32%   0.975    3215
    3.14       49620    8240      8242      100.0%       9.2%      8.7%    49619   17.14    10.1%     6.2%    19%   0.876    3847
    2.81       59388    9379      9379      100.0%      17.7%     18.1%    59387   10.44    19.3%    12.3%     0%   0.736    4410
    2.56       65652   10308     10310      100.0%      34.6%     39.1%    65652    6.08    37.7%    23.6%    -1%   0.680    4872
    2.37       71744   11258     11259      100.0%      71.3%     83.8%    71744    3.23    77.6%    52.1%    -2%   0.652    5352
    2.22       74888   12065     12082       99.9%     111.0%    116.9%    74888    1.98   121.2%    86.9%     2%   0.718    5753
    2.09       65727   12386     12874       96.2%     151.3%    176.1%    65517    1.12   168.0%   148.4%    -3%   0.631    5797
   total      474209   79003     79550       99.3%      10.3%     11.0%   473975    9.44    11.3%    17.2%    13%   0.772   36889


NUMBER OF REFLECTIONS IN SELECTED SUBSET OF IMAGES  492346
NUMBER OF REJECTED MISFITS                           17898
NUMBER OF SYSTEMATIC ABSENT REFLECTIONS                141
NUMBER OF ACCEPTED OBSERVATIONS                     474307
NUMBER OF UNIQUE ACCEPTED REFLECTIONS                79022

which is much worse than the spacegroup 19 statistics (compare the ISa values - they differ by a factor of 2 !) so there may be something wrong with some assumptions we were making ...

Identifying a possible cause

The easiest thing one can do is to inspect INTEGRATE.LP - this lists scale factor, beam divergence and mosaicity for every reflection. There's a jiffy called "scalefactors" which grep's the relevant lines from INTEGRATE.LP ("scalefactors > scales.log"). This shows the scale factor (column 3): 1y13-e1-scales.png

demonstrating that "something happens" between frame 372 and 373 (of course one has to look at the table to find the exact numbers).

It should be noted that any abrupt change in conditions during the experiment is going to spoil the resulting data in one way or another. This is most true for a SAD experiment which is supposed to give accurate values for the tiny differences in intensities between Friedel-related reflections.

A solution

At this point it is good to look at the data for experiment E2. Here, we find exactly the same problems of bad ISa and high "STANDARD DEVIATION OF SPOT POSITION (PIXELS)" when reducing frames 1-591 in one run of xds.

With this knowledge, we are lead, for E1, to reduce frames 1-372 and 373-592 separately, in spacegroup 96. For E2, we use frames 1-369 and 371-591, respectively. Frame E2-370 has a very high scale factor so we leave it out altogether.

This is also a good time to closely inspect the headers of the frames:

% grep --binary-files=text DATE j1603b3PK_1_E1_37?.img

gives

j1603b3PK_1_E1_370.img:DATE=Sun Jun 27 08:55:51 2004;
j1603b3PK_1_E1_371.img:DATE=Sun Jun 27 08:56:00 2004;
j1603b3PK_1_E1_372.img:DATE=Sun Jun 27 08:56:08 2004;
j1603b3PK_1_E1_373.img:DATE=Sun Jun 27 09:19:45 2004;
j1603b3PK_1_E1_374.img:DATE=Sun Jun 27 09:19:54 2004;
j1603b3PK_1_E1_375.img:DATE=Sun Jun 27 09:20:02 2004;
j1603b3PK_1_E1_376.img:DATE=Sun Jun 27 09:20:10 2004;
j1603b3PK_1_E1_377.img:DATE=Sun Jun 27 09:20:58 2004;
j1603b3PK_1_E1_378.img:DATE=Sun Jun 27 09:21:08 2004;
j1603b3PK_1_E1_379.img:DATE=Sun Jun 27 09:21:17 2004;

and

% grep --binary-files=text DATE j1603b3PK_1_E2_3[67]?.img

gives

j1603b3PK_1_E2_366.img:DATE=Sun Jun 27 08:55:15 2004;
j1603b3PK_1_E2_367.img:DATE=Sun Jun 27 08:55:23 2004;
j1603b3PK_1_E2_368.img:DATE=Sun Jun 27 08:55:32 2004;
j1603b3PK_1_E2_369.img:DATE=Sun Jun 27 08:56:19 2004;
j1603b3PK_1_E2_370.img:DATE=Sun Jun 27 08:56:28 2004;
j1603b3PK_1_E2_371.img:DATE=Sun Jun 27 09:19:26 2004;
j1603b3PK_1_E2_372.img:DATE=Sun Jun 27 09:19:34 2004;
j1603b3PK_1_E2_373.img:DATE=Sun Jun 27 09:20:22 2004;
j1603b3PK_1_E2_374.img:DATE=Sun Jun 27 09:20:30 2004;
j1603b3PK_1_E2_375.img:DATE=Sun Jun 27 09:20:38 2004;
j1603b3PK_1_E2_376.img:DATE=Sun Jun 27 09:20:47 2004;

thus proving that both datasets were interrupted for 20 minutes around frame 370.

Interestingly, both datasets appear to be collected at the same time, but at different wavelengths (E1 at 0.9794 Å, E2 at 0.9184 Å), and yet the individual parts merge as follows: using the following XSCALE.INP:

UNIT_CELL_CONSTANTS=103.316   103.316   131.456  90.000  90.000  90.000
SPACE_GROUP_NUMBER=96
OUTPUT_FILE=temp.ahkl
INPUT_FILE=../e1_1-372/XDS_ASCII.HKL
INPUT_FILE=../e1_373-592/XDS_ASCII.HKL
INPUT_FILE=../e2_1-369/XDS_ASCII.HKL
INPUT_FILE=../e2_371-591/XDS_ASCII.HKL

and running xscale, we obtain in XSCALE.LP:

    CORRELATIONS BETWEEN INPUT DATA SETS AFTER CORRECTIONS

DATA SETS  NUMBER OF COMMON  CORRELATION   RATIO OF COMMON   B-FACTOR
 #i   #j     REFLECTIONS     BETWEEN i,j  INTENSITIES (i/j)  BETWEEN i,j

   1    2       15943           0.978            1.0002         0.0106
   1    3       22366           1.000            1.0012        -0.0008
   2    3       15801           0.977            0.9983         0.0557
   1    4       15648           0.979            0.9988         0.0541
   2    4       14862           0.999            1.0024        -0.0007
   3    4       15524           0.978            0.9999        -0.0015

which means that e1_1-372 correlates well (1.000) with e2_1-369, and e1_373-59 well (0.999) with e2_371-591, but the crosswise correlations are consistently low (0.978, 0.977, 0.979, 0.978). The adjustment to the error model proves this:

    a        b          ISa    ISa0   INPUT DATA SET
6.112E+00  1.429E-03   10.70   22.37 ../e1_1-372/XDS_ASCII.HKL                         
1.074E+01  1.825E-03    7.14   23.79 ../e1_373-592/XDS_ASCII.HKL                       
5.707E+00  1.621E-03   10.40   22.82 ../e2_1-369/XDS_ASCII.HKL                         
8.547E+00  1.796E-03    8.07   24.17 ../e2_371-591/XDS_ASCII.HKL                       

telling us that "if we merge these datasets together, their error estimates have to be increased a lot". However, if we switch to

UNIT_CELL_CONSTANTS=103.316   103.316   131.456  90.000  90.000  90.000
SPACE_GROUP_NUMBER=96

OUTPUT_FILE=firstparts.ahkl
INPUT_FILE=../e1_1-372/XDS_ASCII.HKL
INPUT_FILE=../e2_1-369/XDS_ASCII.HKL

OUTPUT_FILE=secondparts.ahkl
INPUT_FILE=../e1_373-592/XDS_ASCII.HKL
INPUT_FILE=../e2_371-591/XDS_ASCII.HKL

we obtain

    a        b          ISa    ISa0   INPUT DATA SET
6.120E+00  3.673E-04   21.09   22.37 ../e1_1-372/XDS_ASCII.HKL                         
5.713E+00  3.819E-04   21.41   22.82 ../e2_1-369/XDS_ASCII.HKL                         
5.639E+00  3.151E-04   23.72   23.79 ../e1_373-592/XDS_ASCII.HKL                       
5.289E+00  3.258E-04   24.09   24.17 ../e2_371-591/XDS_ASCII.HKL                       

proving that the second parts of datasets E1 and E2 should be treated separately from the first parts.

Upon inspection of the cell parameters, we find that the cell axes of the second "halfs" are shorter by a factor of 0.9908 when compared with the first parts. This suggests that they were collected at a longer wavelength, or that radiation damage changed the cell parameters during the 20-minute break - usually it makes them longer (Ravelli et al. (2002), J. Synchrotron Rad. 9, 355-360), but this may be the exception to the rule! Maybe the crystal even was exposed to the beam during that time, in an attempt to try radiation-damage induced phasing (see e.g. Ravelli et al Structure 11 (2003), 217-220).

The almost-simultaneous DATEs in the headers may be explained by a wavelength-switching measuring strategy which alternatingly collects 4 frames at one wavelength as E1, then changes the wavelength and collects 4 frames into E2.

So this little detective work appears to give us useful information about what happened in the morning of Sunday June 27, 2004 at ALS beamline 821 - but some questions remain.

Further analysis of datasets E1 and E2

Here, we try to learn more about the constituents of "firstparts".

Running "xdsstat > XDSSTAT.LP" in the e1_1-372 and e2_1-369 directories, we obtain statistics output not available from CORRECT. We open XDSSTAT.LP with the CCP4 program "loggraph", and take a look at misfits.pck, rf.pck, and the other files produced by xdsstat, using VIEW or XDS-Viewer:

E1 1-372-xdsstat1.png

Reflections and misfits, by frame - looks normal

E1 1-372-xdsstat2.png

Intensity and sigma by frame - looks normal

E1 1-372-xdsstat3.png

"partiality" and profile agreement, by frame - looks good but it's clear that the profiles at high frame number agree worse with the average profiles, possibly due to radiation damage

E1 1-372-xdsstat4.png

R_meas, by frame, clearly showing good R_meas in the middle of the dataset

E1 1-372-xdsstat-raddam.png

R_d - an R-factor which directly depends on radiation damage. This is calculated as a function of frame number difference and the linear rise indicates significant radiation damage that should be correctable in XSCALE, using the CRYSTAL_NAME keyword.

E1 1-372-misfits.png

misfits mapped on the detector, showing ice rings.

E1 1-372-rf.png

R_meas mapped on the detector, showing elevated R_meas at the location of the ice rings.

Solving the structure with pseudo-SAD

It appears reasonable to discard the "second parts" since they are strongly influenced by radiation damage. Then, we could

  1. merge together (into one output file) the two first parts of E1 and E2, thus obtaining a single pseudo-SAD dataset. The reason for doing this is that the anomalous signal of both datasets is so strong, and their (isomorphous) difference is weak (after all, the correlation coefficient is 1.000 !)
  2. keep the first parts of E1 (inflection, according to the documentation) and E2 (high-enery remote) separate, and treat them as MAD (or rather, DAD).

First try

Let's look at the XSCALE statistics for the merged-together "firstparts":

      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

    9.40        6122     844       883       95.6%       2.9%      3.5%     6111   54.76     3.2%     1.4%    79%   2.137     313
    6.64       12037    1611      1621       99.4%       2.9%      3.6%    12035   51.54     3.1%     1.5%    80%   2.259     684
    5.43       15348    2065      2086       99.0%       3.5%      3.7%    15347   47.79     3.7%     1.7%    78%   2.294     908
    4.70       18714    2487      2498       99.6%       3.0%      3.7%    18711   49.55     3.2%     1.5%    72%   1.712    1120
    4.20       21104    2797      2821       99.1%       3.1%      3.7%    21102   47.24     3.3%     1.7%    72%   1.727    1271
    3.84       23316    3095      3117       99.3%       3.8%      4.0%    23313   42.74     4.1%     2.1%    65%   1.617    1420
    3.55       25693    3345      3366       99.4%       4.4%      4.5%    25693   37.93     4.7%     2.6%    50%   1.411    1548
    3.32       28017    3633      3653       99.5%       5.2%      5.2%    28015   32.89     5.6%     3.6%    40%   1.335    1687
    3.13       30266    3842      3848       99.8%       7.2%      7.2%    30264   25.87     7.7%     4.8%    36%   1.158    1797
    2.97       32595    4114      4118       99.9%      10.4%     10.4%    32594   19.26    11.1%     7.7%    30%   1.068    1925
    2.83       34384    4315      4320       99.9%      14.3%     14.8%    34382   14.88    15.3%    10.3%    20%   0.937    2031
    2.71       35654    4475      4478       99.9%      18.3%     19.1%    35652   12.13    19.5%    13.1%    15%   0.891    2110
    2.61       37307    4705      4710       99.9%      27.5%     28.8%    37304    8.44    29.4%    19.8%    11%   0.834    2224
    2.51       38997    4893      4896       99.9%      35.5%     38.0%    38997    6.78    38.0%    26.0%    10%   0.817    2318
    2.43       40036    5026      5027      100.0%      51.3%     55.1%    40032    4.92    54.8%    38.0%     2%   0.738    2387
    2.35       39975    5180      5222       99.2%      71.3%     68.9%    39967    3.78    76.4%    52.7%    21%   0.887    2446
    2.28       42041    5385      5423       99.3%      93.7%     93.1%    42037    2.90   100.3%    66.7%    11%   0.798    2548
    2.21       43012    5538      5541       99.9%      85.7%     88.3%    43011    2.87    91.8%    58.8%    10%   0.818    2644
    2.16       42610    5701      5703      100.0%     113.6%    120.7%    42607    2.13   122.0%    85.4%     4%   0.722    2724
    2.10       38996    5634      5912       95.3%     146.1%    153.9%    38944    1.50   157.8%   122.7%     3%   0.711    2639
   total      606224   78685     79243       99.3%       6.7%      7.2%   606118   16.88     7.2%    12.0%    29%   1.055   36744

The anomalous correlation is good at low resolution, though not outstanding. At high resolution it rises again but this is presumably due to the ice rings.

I like to use hkl2map which runs SHELXC, SHELXD and SHELXE from its GUI. Before doing so, we have to run XDSCONV with the following XDSCONV.INP:

INPUT_FILE=firstparts.hkl
OUTPUT_FILE=temp.hkl SHELX

First, the shelxc output which shows that these data are quite good: E1+e2 firstparts-i-sigi-resol.png E1+e2 firstparts-self-anomcc.png And then we show the result of 100 trials at substructure solution of shelxd, trying to find 3 Se atoms at 30 - 3.3Å resolution (I also tried 3.0 3.1 3.2 3.4 3.5 Å but 3.3 Å was best). E1+e2 firstparts-ccall-ccweak.png E1+e2 firstparts-occ-vs-peak.png

This looks reasonable although the absolute value of CCall is so low that there is little hope that the structure can be solved with this amount of information. And indeed, SHELXE did not show a difference between the two hands (in fact we even know that the "original hand" is the correct one since the inverted had would correspond to spacegroup #92 !).

Second try: correcting radiation damage by 0-dose extrapolation

Since we noted significant radiation damage we could try to correct that. All we have to do is ask XSCALE to do zero-dose extrapolation:

UNIT_CELL_CONSTANTS=103.316   103.316   131.456  90.000  90.000  90.000
SPACE_GROUP_NUMBER=96

OUTPUT_FILE=temp.ahkl
INPUT_FILE=../e1_1-372/XDS_ASCII.HKL
CRYSTAL_NAME=a
INPUT_FILE=../e2_1-369/XDS_ASCII.HKL
CRYSTAL_NAME=a

As a result we obtain in XSCALE.LP:


 ******************************************************************************
          RESULTS FROM ZERO-DOSE EXTRAPOLATION OF REFLECTION INTENSITIES

                       for reference on this subject see:
 K. Diederichs, S. McSweeney & R.B.G. Ravelli, Acta Cryst. D59, 903-909(2003).
 "Zero-dose extrapolation as part of macromolecular synchrotron data reduction"
 ******************************************************************************

 Radiation damage can lead to localized modifications of the structure.
 To correct for this effect, XSCALE modifies the intensity measurements
 I(h,i) by individual correction factors,

                      exp{-b(h)*dose(h,i)}

 where h,i denotes the i-th observation with unique reflection indices
 h, and dose(h,i) the X-ray dose accumulated by the crystal when the
 reflection was recorded. Assuming a constant dose for each image
 (dose_rate), the accumulated dose when recording image_number(i), on
 which I(h,i) was observed, is then

 dose(h,i) = starting_dose + dose_rate * (image_number(i)-first_image)

 The decay factor b(h) is determined from the assumption that symmetry
 related reflections in a data set taken from the same crystal should
 have the same intensity after correction. Moreover, b(h) is assumed to
 be the same for Friedel-pairs and independent of the X-ray wavelength.

 To avoid overfitting the data, XSCALE starts with the hypothesis that
 b(h)=0 and rejects this assumption if its probability is below 10.0%.



 CORRELATION OF COMMON DECAY-FACTORS BETWEEN INPUT DATA SETS
 -----------------------------------------------------------


 First  INPUT_FILE= ../e2_1-369/XDS_ASCII.HKL                         
      CRYSTAL_NAME= a                                                 
 Second INPUT_FILE= ../e1_1-372/XDS_ASCII.HKL                         
      CRYSTAL_NAME= a                                                 

 RESOLUTION    NUMBER    CORRELATION
   LIMIT      OF PAIRS      FACTOR

     9.40         210        0.955
     6.64         441        0.955
     5.43         587        0.940
     4.70         692        0.969
     4.20         750        0.949
     3.84         836        0.920
     3.55         809        0.942
     3.32         775        0.925
     3.13         663        0.888
     2.97         557        0.837
     2.83         375        0.681
     2.71         302        0.812
     2.61         212        0.625
     2.51         163        0.508
     2.43          95        0.291
     2.35         139        0.722
     2.28         110        0.688
     2.21          91        0.734
     2.16          88        0.561
     2.10          54        0.126
    total        7949        0.788


           X-RAY DOSE PARAMETERS USED FOR EACH INPUT DATA SET
           --------------------------------------------------


 CRYSTAL_NAME= a                                                 
        STARTING_DOSE             DOSE_RATE       NAME OF INPUT FILE
     initial    refined      initial    refined

   0.000E+00   8.557E+00   1.000E+00   1.000E+00  ../e1_1-372/XDS_ASCII.HKL                         
   0.000E+00   0.000E+00   1.000E+00   1.024E+00  ../e2_1-369/XDS_ASCII.HKL                         


           STATISTICS OF 0-DOSE CORRECTED DATA FROM EACH CRYSTAL
           -----------------------------------------------------

 NUNIQUE = Number of unique reflections with enough symmetry-
           related observations to determine a decay factor b(h)
 N0-DOSE = Number of 0-dose extrapolated unique reflections
 NERROR  = Number of unique extrapolated reflections expected
           to be overfitted. A large ratio of N0-DOSE/NERROR
           justifies the data correction as carried out here.
 S_corr  = mean value of Sigma(I) for 0-dose extrapolated data
 S_norm  = mean value of Sigma(I) for the same data but
           without 0-dose extrapolation.
 NFREE   = degrees of freedom for calculating S_corr


 CRYSTAL_NAME= a                                                 

 RESOLUTION  NUNIQUE  N0-DOSE  N0-DOSE/   S_corr/    NFREE
   LIMIT                        NERROR    S_norm
     9.40       496     378      68.0       0.543     3180
     6.64       908     703      78.9       0.554     6245
     5.43      1140     894      77.0       0.574     8064
     4.70      1351    1040      77.4       0.599     9671
     4.20      1518    1133      69.9       0.620    10585
     3.84      1665    1187      73.9       0.630    11129
     3.55      1787    1220      65.1       0.671    11917
     3.32      1941    1289      58.1       0.690    12728
     3.13      2042    1172      49.8       0.717    11877
     2.97      2182    1103      48.1       0.750    11498
     2.83      2281     911      40.1       0.798     9662
     2.71      2352     812      34.2       0.825     8611
     2.61      2467     702      34.1       0.848     7383
     2.51      2566     627      31.5       0.875     6595
     2.43      2624     499      31.2       0.895     5295
     2.35      2709     629      31.6       0.888     6240
     2.28      2821     603      28.5       0.893     6147
     2.21      2880     560      32.4       0.905     5758
     2.16      2959     448      30.3       0.907     4394
     2.10      2860     413      29.9       0.924     3745
    total     41549   16323      46.8       0.739   160724

 ******************************************************************************
              SCALING FACTORS FOR Sigma(I) AS FUNCTION OF RESOLUTION
 ******************************************************************************

 SCALING FACTORS FOR Sigma(I) FOR DATA SET ../e1_1-372/XDS_ASCII.HKL                         
                                   RESOLUTION (ANGSTROM)  
         10.33  6.12  4.76  4.03  3.56  3.23  2.97  2.76  2.60  2.46  2.34  2.23  2.14
 FACTOR   0.94  0.96  0.88  0.93  0.99  0.98  0.99  0.99  0.99  0.98  1.10  1.00  0.99

 SCALING FACTORS FOR Sigma(I) FOR DATA SET ../e2_1-369/XDS_ASCII.HKL                         
                                   RESOLUTION (ANGSTROM)  
         10.32  6.11  4.76  4.03  3.56  3.22  2.97  2.76  2.60  2.46  2.34  2.23  2.14
 FACTOR   0.96  0.98  0.89  0.94  1.01  1.01  1.02  1.01  1.00  0.99  1.11  1.02  0.98


 ******************************************************************************
  STATISTICS OF SCALED OUTPUT DATA SET : temp.ahkl                                         
  FILE TYPE:         XDS_ASCII      MERGE=FALSE          FRIEDEL'S_LAW=FALSE

      1270 OUT OF    607179 REFLECTIONS REJECTED
    605909 REFLECTIONS ON OUTPUT FILE 

 ******************************************************************************
 DEFINITIONS:
 R-FACTOR
 observed = (SUM(ABS(I(h,i)-I(h))))/(SUM(I(h,i)))
 expected = expected R-FACTOR derived from Sigma(I)

 COMPARED = number of reflections used for calculating R-FACTOR
 I/SIGMA  = mean of intensity/Sigma(I) of unique reflections
            (after merging symmetry-related observations)
 Sigma(I) = standard deviation of reflection intensity I
            estimated from sample statistics

 R-meas   = redundancy independent R-factor (intensities)
 Rmrgd-F  = quality of amplitudes (F) in the scaled data set
            For definition of R-meas and Rmrgd-F see 
            Diederichs & Karplus (1997), Nature Struct. Biol. 4, 269-275.

 Anomal   = mean correlation factor between two random subsets
  Corr      of anomalous intensity differences
 SigAno   = mean anomalous difference in units of its estimated
            standard deviation (|F(+)-F(-)|/Sigma). F(+), F(-)
            are structure factor estimates obtained from the
            merged intensity observations in each parity class.
  Nano    = Number of unique reflections used to calculate
            Anomal_Corr & SigAno. At least two observations
            for each (+ and -) parity are required.

       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

     9.40        6095     844       883       95.6%       2.0%      2.6%     6084   73.41     2.1%     0.9%    87%   2.706     313
     6.64       12006    1611      1621       99.4%       2.0%      2.8%    12004   68.81     2.1%     1.0%    84%   2.555     684
     5.43       15339    2065      2086       99.0%       2.2%      2.8%    15338   63.28     2.4%     1.2%    82%   2.409     908
     4.70       18697    2486      2498       99.5%       1.9%      2.6%    18694   70.84     2.1%     1.0%    75%   1.855    1120
     4.20       21080    2796      2821       99.1%       2.0%      2.7%    21078   66.87     2.1%     1.1%    67%   1.727    1270
     3.84       23300    3094      3117       99.3%       2.5%      3.0%    23297   58.10     2.7%     1.5%    64%   1.551    1420
     3.55       25676    3344      3366       99.3%       3.1%      3.6%    25676   48.56     3.4%     1.9%    50%   1.326    1548
     3.32       28013    3633      3653       99.5%       3.9%      4.3%    28011   41.76     4.1%     2.8%    37%   1.244    1687
     3.13       30254    3841      3848       99.8%       5.7%      6.0%    30252   32.18     6.1%     4.1%    35%   1.125    1796
     2.97       32595    4114      4118       99.9%       8.8%      9.1%    32594   23.53     9.4%     6.8%    26%   1.038    1925
     2.83       34368    4313      4320       99.8%      12.8%     13.3%    34366   17.65    13.6%     9.5%    21%   0.989    2030
     2.71       35627    4472      4478       99.9%      16.9%     17.4%    35625   14.15    18.1%    12.2%    18%   0.965    2108
     2.61       37300    4704      4710       99.9%      25.8%     26.4%    37297    9.70    27.6%    19.3%    16%   0.930    2223
     2.51       38975    4890      4896       99.9%      33.8%     34.9%    38975    7.68    36.1%    24.1%    14%   0.888    2315
     2.43       39971    5019      5027       99.8%      49.1%     50.8%    39967    5.47    52.5%    37.2%     8%   0.810    2380
     2.35       39968    5179      5222       99.2%      67.9%     67.5%    39960    4.07    72.7%    50.4%    25%   0.927    2445
     2.28       42067    5388      5423       99.4%      89.9%     94.3%    42063    3.03    96.2%    63.5%    16%   0.796    2548
     2.21       43011    5538      5541       99.9%      82.3%     83.3%    43010    3.16    88.1%    57.9%    14%   0.871    2644
     2.16       42577    5697      5703       99.9%     108.5%    112.2%    42574    2.37   116.6%    83.1%     3%   0.760    2720
     2.10       38988    5633      5912       95.3%     142.1%    144.2%    38936    1.67   153.5%   119.2%     6%   0.772    2638
    total      605907   78661     79243       99.3%       5.5%      6.1%   605801   21.72     5.9%    11.3%    27%   1.095   36722

We note that the "CORRELATION OF COMMON DECAY-FACTORS BETWEEN INPUT DATA SETS" are really high which confirms the hypothesis that this is a valid procedure to perform.

Comparison of the last table with that of the previous paragraph, i.e. without zero-dose extrapolation, shows that the I/sigma, the anomalous correlation coefficients and the SigAno are significantly higher. Does this translate into better structure solution? It does:

1y13-raddam-ccall-ccweak-raddam.png 1y13-raddam-site-occ-raddam.png 1y13-raddam-contrast-raddam.png

Automatically building the main chain of 452 out of 519 residues

Based on the sites obtained by SHELXD, we run

shelxe.beta -a -q -h -b -s0.585 -m40 raddam raddam_fa

This already builds a significant number of residues, but also gives an improved list of heavy atom sites - there are actually 6 sites instead of the 5 that SHELXD wrote out (yes, we had asked SHELXD for 3 sites since there are 3 Met residues, but SHELXD as always was smarter than we are). We "mv raddam.hat raddam_fa.res" for another run of SHELXE:

shelxe.beta -a -q -h6 -b -s0.585 -m40 -n3 raddam raddam_fa

and get

   452 residues left after pruning, divided into chains as follows:
 A:  15   B:   5   C:  22   D:  22   E:  27   F:  62   G: 263   H:  36

 CC for partial structure against native data =  39.83 %

 ------------------------------------------------------------------------------

 Global autotracing cycle   4

 <wt> = 0.300, Contrast = 0.447, Connect. = 0.705 for dens.mod. cycle 1
 <wt> = 0.300, Contrast = 0.660, Connect. = 0.781 for dens.mod. cycle 2
 <wt> = 0.300, Contrast = 0.723, Connect. = 0.801 for dens.mod. cycle 3
 <wt> = 0.300, Contrast = 0.762, Connect. = 0.807 for dens.mod. cycle 4
 Pseudo-free CC = 64.88 %
 <wt> = 0.300, Contrast = 0.785, Connect. = 0.810 for dens.mod. cycle 5
 <wt> = 0.300, Contrast = 0.806, Connect. = 0.813 for dens.mod. cycle 6
 <wt> = 0.300, Contrast = 0.820, Connect. = 0.815 for dens.mod. cycle 7
 <wt> = 0.300, Contrast = 0.831, Connect. = 0.817 for dens.mod. cycle 8
 <wt> = 0.300, Contrast = 0.839, Connect. = 0.819 for dens.mod. cycle 9
 Pseudo-free CC = 69.74 %
 <wt> = 0.300, Contrast = 0.845, Connect. = 0.820 for dens.mod. cycle 10
 <wt> = 0.300, Contrast = 0.849, Connect. = 0.821 for dens.mod. cycle 11
 <wt> = 0.300, Contrast = 0.851, Connect. = 0.822 for dens.mod. cycle 12
 <wt> = 0.300, Contrast = 0.853, Connect. = 0.823 for dens.mod. cycle 13
 <wt> = 0.300, Contrast = 0.854, Connect. = 0.823 for dens.mod. cycle 14
 Pseudo-free CC = 70.80 %
 <wt> = 0.300, Contrast = 0.854, Connect. = 0.824 for dens.mod. cycle 15
 <wt> = 0.300, Contrast = 0.855, Connect. = 0.824 for dens.mod. cycle 16
 <wt> = 0.300, Contrast = 0.855, Connect. = 0.824 for dens.mod. cycle 17
 <wt> = 0.300, Contrast = 0.854, Connect. = 0.824 for dens.mod. cycle 18
 <wt> = 0.300, Contrast = 0.854, Connect. = 0.824 for dens.mod. cycle 19
 Pseudo-free CC = 71.03 %
 <wt> = 0.300, Contrast = 0.854, Connect. = 0.824 for dens.mod. cycle 20

 Estimated mean FOM and mapCC as a function of resolution
 d    inf - 4.62 - 3.64 - 3.17 - 2.88 - 2.67 - 2.51 - 2.38 - 2.27 - 2.18 - 2.11
 <FOM>   0.736  0.786  0.768  0.721  0.701  0.681  0.618  0.595  0.587  0.540
 <mapCC> 0.862  0.932  0.946  0.934  0.924  0.924  0.922  0.913  0.882  0.858
 N        4206   4227   4214   4135   4185   4207   4292   4406   4320   3702

 Estimated mean FOM = 0.674   Pseudo-free CC = 71.18 %

 Density (in map sigma units) at input heavy atom sites

  Site     x        y        z     occ*Z    density
    1   0.2276   0.7578   0.1189  34.0000    29.98
    2   0.1568   0.6345   0.3049  32.2898    30.44
    3   0.1767   0.5344   0.2160  32.2388    29.67
    4   0.3059   0.4535   0.1297  26.0746    23.51
    5   0.0280   0.8243   0.1410  22.7324    21.02
    6   0.0383   0.9748   0.0492  21.5050    21.18

 Site    x       y       z  h(sig) near old  near new
   1  0.1569  0.6345  0.3048  30.4  2/0.02  9/13.36 3/15.73 2/19.52 7/22.13
   2  0.2278  0.7578  0.1188  30.0  1/0.02  1/19.52 6/21.97 7/22.48 9/25.02
   3  0.1767  0.5345  0.2158  29.7  3/0.03  9/2.90 1/15.73 4/19.45 2/26.88
   4  0.3060  0.4536  0.1292  23.5  4/0.07  3/19.45 9/21.16 8/26.49 5/26.83
   5  0.0382  0.9748  0.0490  21.2  6/0.02  8/2.63 8/15.66 5/15.88 6/19.80
   6  0.0278  0.8240  0.1416  21.1  5/0.08  5/19.80 8/21.59 7/21.87 2/21.97
   7  0.1854  0.9571  0.1787  -5.0  5/21.86  6/21.87 1/22.13 2/22.48 8/22.57
   8  0.0427  0.9993  0.0530  -5.0  6/2.62  5/2.63 8/15.31 5/15.66 6/21.59
   9  0.1787  0.5611  0.2228  -4.7  3/2.91  3/2.90 1/13.36 4/21.16 2/25.02

At this point the structure is obviously solved, and we could use buccaneer or Arp/wArp to add side chains and the rest of the model. 3-fold NCS surely helps!

Could we do better?

Yes, of course (as always). I can think of four things to try:

  • an optimization round of running xds for the two datasets
  • using a negative offset for STARTING_DOSE in XSCALE.INP, as documented in the XSCALE wiki article.
  • use MERGE=TRUE in XDSCONV.INP. I tried it and this gives 20 solutions with CCall+CCweak > 25 out of 1000 trials, whereas MERGE=FALSE (the default) gives only 4 solutions! Update Sep 2011: the beta-test version of SHELXC should have a fix for this.

better phases from DAD (Double Anomalous Dispersion)

The reason why pseudo-SAD is described here first is that, historically, I did it first since I thought that the wavelength could not realistically be changed within 3 seconds, and I therefore thought that the headers were wrong and this would not actually be a two-wavelength experiment. Along these lines, I interpreted the correlation coefficient of 1.0 between the E1 and E2 first parts as indicating that no isomorphous difference exists.

In a discussion with Gerard Bricogne and Clemens Vonrhein after the ACA2011 workshop it turned out that my theory, which claims that E1 and E2 are actually the same wavelength, is wrong. This was investigated by looking at the difference map (obtained using phenix.fobs_minus_fobs_map) of E1 and E2 (taking the first parts in each case) phased with the 1y13 model, which shows three strong (14-19 sigma) peaks. The fact that the 1-370 pieces merge so well seems to be a consequence of the fact that the anomalous signal of the two wavelengths is so similar, and the dispersive difference between the wavelengths does not significantly decrease the high correlation coefficient in data scaling.

Thus even better phasing would be obtained by keeping the wavelengths separate and doing MAD (in fact DAD) - but zero-dose extrapolation could and should be done in the same way. I've therefore continued the analysis in 1Y13-DAD.