1Y13

The data for this project were provided by Jürgen Bosch (SGPP). The structure is deposited in the PDB, with a resolution of 2.2 A in spacegroup P4(3)2(1)2 (#96), solved with SAD.

dataset E1

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

INCLUDE_RESOLUTION_RANGE=50 2.1
VALUE_RANGE_FOR_TRUSTED_DETECTOR_PIXELS=8000. 30000. 

and ran xds again. 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. Please note that the "UNIT CELL PARAMETERS" and the "E.S.D. OF CELL PARAMETERS" lines give a difference between the a and the b axis of 0.359 A, whereas the sum of their E.S.D.s is only 0.13+0.086 = 0.22 A.

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:

• CORRECT obviously indicates an orthorhombic spacegroup.
• the number of MISFITS is higher than 1%. Running "xdsstat > XDSSTAT.LP" we obtain, among other files, the file "misfits.pck" which can be visualized using VIEW or XDS-Viewer. This clearly shows that many misfits are due to faint high-resolution ice rings - so nothing to worry about.

To my surprise, pointless 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

( 92) 0.823 0.823 00l: l=4n, h00: h=2n (zones 1,2)

( 96) 0.823 0.823 00l: l=4n, h00: h=2n (zones 1,2) ..........

( 90) 0.095 0.095 h00: h=2n (zone 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. Running CORRECT in #96, 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