Trypsin inhibitor ACA2014

From XDSwiki

These data (courtesy Alex Wlodawer) were collected at Argonne on Nov 8, 2013 . Data are at ftp://turn5.biologie.uni-konstanz.de/pub/datasets/ACA2014_Trypsin_with_inhibitor/ .

IDXREF result:

   #  COORDINATES OF REC. BASIS VECTOR    LENGTH   1/LENGTH

    1  -0.0017685 0.0011854-0.0061735  0.0065303     153.13
    2  -0.0189786-0.0105844 0.0034665  0.0220053      45.44
    3  -0.0094418 0.0190007 0.0059961  0.0220483      45.36

 CLUSTER COORDINATES AND INDICES WITH RESPECT TO REC. LATTICE BASIS VECTORS 

   #  COORDINATES OF VECTOR CLUSTER   FREQUENCY       CLUSTER INDICES   
    1 -0.0018142 0.0012260-0.0063005      365.      1.02      0.00      0.00
    2 -0.0129933 0.0213575-0.0063589      354.      2.00      0.00      1.00
    3 -0.0302099 0.0095826 0.0032290      349.      1.01      1.00      1.00
    4 -0.0172226-0.0117556 0.0095526      348.     -0.99      1.00     -0.00
    5  0.0207798 0.0093114 0.0028027      344.     -1.02     -1.00     -0.00
    6  0.0319377-0.0108030 0.0028681      334.     -2.00     -1.00     -1.00
    7  0.0190207 0.0105298-0.0032763      334.     -0.03     -1.00     -0.00
    8  0.0379514 0.0211079-0.0069708      319.      0.00     -2.00     -0.00
    9  0.0491599 0.0009718-0.0066807      316.     -1.01     -2.00     -1.00
   10  0.0111596-0.0201294 0.0000315      301.     -0.98     -0.00     -1.00
 ...

  INDEX_   QUALITY  DELTA    XD       YD       X       Y       Z       DH      DK      DL
  ORIGIN

  0  0  0      1.0    0.0   1970.8   2043.3 -0.0000  0.0000  1.0000    0.04    0.04    0.16
  0  0  1      7.7    0.2   1976.3   2035.0  0.0017 -0.0026  1.0000    0.12    0.04    0.71
  0  0 -1      9.9    0.2   1965.2   2051.7 -0.0018  0.0027  1.0000    0.14    0.04    0.82

 SELECTED:     INDEX_ORIGIN=  0  0  0


 ***** REFINED SOLUTION BASED ON INDEXED REFLECTIONS IN SUBTREE # 1 *****

 REFINED VALUES OF DIFFRACTION PARAMETERS DERIVED FROM   2694 INDEXED SPOTS
 REFINED PARAMETERS:   AXIS BEAM CELL ORIENTATION
 STANDARD DEVIATION OF SPOT    POSITION (PIXELS)     5.71
 STANDARD DEVIATION OF SPINDLE POSITION (DEGREES)    1.14
 SPACE GROUP NUMBER      1
 UNIT CELL PARAMETERS     45.229    45.491   150.915  90.326  89.651  89.801
 REC. CELL PARAMETERS   0.022110  0.021983  0.006626  89.673  90.350  90.201
 COORDINATES OF UNIT CELL A-AXIS   -19.272    38.924    12.615
 COORDINATES OF UNIT CELL B-AXIS    39.293    21.868    -6.882
 COORDINATES OF UNIT CELL C-AXIS   -41.017    27.007  -142.701
 CRYSTAL MOSAICITY (DEGREES)     0.200
 LAB COORDINATES OF ROTATION AXIS  0.999979  0.006101  0.002060
 DIRECT BEAM COORDINATES (REC. ANGSTROEM)  -0.000068  0.000063  1.000000
 DETECTOR COORDINATES (PIXELS) OF DIRECT BEAM    1970.66   2043.36
 DETECTOR ORIGIN (PIXELS) AT                     1970.87   2043.16
 CRYSTAL TO DETECTOR DISTANCE (mm)       230.00
 LAB COORDINATES OF DETECTOR X-AXIS  1.000000  0.000000  0.000000
 LAB COORDINATES OF DETECTOR Y-AXIS  0.000000  1.000000  0.000000


 ***** INDEXING OF OBSERVED SPOTS IN SPACE GROUP #   1 *****
    1903 OUT OF    4254 SPOTS INDEXED.
       0 REJECTED REFLECTIONS (REASON: OVERLAP)
    2351 REJECTED REFLECTIONS (REASON: TOO FAR FROM IDEAL POSITION)
 EXPECTED ERROR IN SPINDLE  POSITION     0.246 DEGREES
 EXPECTED ERROR IN DETECTOR POSITION      1.48 PIXELS


 ***** DIFFRACTION PARAMETERS USED AT START OF INTEGRATION *****

 REFINED VALUES OF DIFFRACTION PARAMETERS DERIVED FROM   1903 INDEXED SPOTS
 REFINED PARAMETERS:   AXIS BEAM CELL ORIENTATION
 STANDARD DEVIATION OF SPOT    POSITION (PIXELS)     1.44
 STANDARD DEVIATION OF SPINDLE POSITION (DEGREES)    0.24
 SPACE GROUP NUMBER      1
 UNIT CELL PARAMETERS     45.268    45.448   151.571  90.109  89.971  89.961
 REC. CELL PARAMETERS   0.022090  0.022003  0.006598  89.891  90.029  90.039
 COORDINATES OF UNIT CELL A-AXIS   -19.295    38.945    12.657
 COORDINATES OF UNIT CELL B-AXIS    39.244    21.790    -7.114
 COORDINATES OF UNIT CELL C-AXIS   -41.012    26.408  -143.507
 CRYSTAL MOSAICITY (DEGREES)     0.200
 LAB COORDINATES OF ROTATION AXIS  0.999989 -0.003220  0.003368
 DIRECT BEAM COORDINATES (REC. ANGSTROEM)  -0.000016  0.000101  1.000000
 DETECTOR COORDINATES (PIXELS) OF DIRECT BEAM    1970.82   2043.48
 DETECTOR ORIGIN (PIXELS) AT                     1970.87   2043.16
 CRYSTAL TO DETECTOR DISTANCE (mm)       230.00
 LAB COORDINATES OF DETECTOR X-AXIS  1.000000  0.000000  0.000000
 LAB COORDINATES OF DETECTOR Y-AXIS  0.000000  1.000000  0.000000

 ...


  LATTICE-  BRAVAIS-   QUALITY  UNIT CELL CONSTANTS (ANGSTROEM & DEGREES)
 CHARACTER  LATTICE     OF FIT      a      b      c   alpha  beta gamma

 *  44        aP          0.0      45.3   45.4  151.6  90.1  90.0  90.0
 *  31        aP          0.3      45.3   45.4  151.6  89.9  90.0  90.0
 *  35        mP          1.2      45.4   45.3  151.6  90.0  90.1  90.0
 *  33        mP          3.5      45.3   45.4  151.6  90.1  90.0  90.0
 *  34        mP          4.1      45.3  151.6   45.4  90.1  90.0  90.0
 *  32        oP          4.4      45.3   45.4  151.6  90.1  90.0  90.0
 *  14        mC          6.3      64.1   64.2  151.6  90.1  90.1  89.8
 *  10        mC          6.7      64.1   64.2  151.6  89.9  90.1  90.2
 *  13        oC          8.0      64.1   64.2  151.6  90.1  90.1  89.8
 *  11        tP          8.4      45.3   45.4  151.6  90.1  90.0  90.0
    41        mC        249.1     306.4   45.4   45.3  90.0  90.0  81.6
 ...

 !!! ERROR !!! INSUFFICIENT PERCENTAGE (< 50%) OF INDEXED REFLECTIONS
 AUTOMATIC DATA PROCESSING STOPPED. AS THE CRITERIA FOR A GOOD
 SOLUTION ARE RATHER STRICT, YOU MAY CHOOSE TO CONTINUE DATA
 PROCESSING AFTER CHANGING THE "JOB="-CARD IN "XDS.INP" TO
 "JOB= DEFPIX INTEGRATE CORRECT".

CORRECT prints:

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

       5      64.6   64.7  154.6  90.0  90.4  90.0     390    24.5       46    10 mC
      75      45.7   45.7  154.6  90.0  90.0  90.0     397    16.0       39    11 tP
      89      45.7   45.7  154.6  90.0  90.0  90.0     298    14.1      138    11 tP
      21      64.6   64.7  154.6  90.0  90.0  90.0     363    21.3       73    13 oC
       5      64.6   64.7  154.6  90.0  90.4  90.0     390    24.5       46    14 mC
       1      45.7   45.8  154.6  90.0  89.4  89.9     430     2.4        6    31 aP
   *  16      45.7   45.8  154.6  90.0  90.0  90.0     348     5.1       88    32 oP
       3      45.7   45.8  154.6  90.0  90.6  90.0     370     5.0       66    33 mP
       3      45.7  154.6   45.8  90.0  90.1  90.0     410     4.6       26    34 mP
       1      45.7   45.8  154.6  90.0  90.6  90.1     430     2.4        6    44 aP

Thus the tetragonal space groups 75 and 89 are significantly worse than the orthorhombics (16 stands for 16 or 17 or 18 or 19).

pointless says:

Analysing rotational symmetry in lattice group P 4/m m m
----------------------------------------------

<!--SUMMARY_BEGIN-->

Scores for each symmetry element

Nelmt  Lklhd  Z-cc    CC        N  Rmeas    Symmetry & operator (in Lattice Cell)

  1   0.834   4.35   1.00      17  0.020     identity
  2   0.922   9.78   0.98     137  0.059 *** 2-fold l ( 0 0 1) {-h,-k,l}
  3   0.922   9.87   0.99     313  0.049 *** 2-fold k ( 0 1 0) {-h,k,-l}
  4   0.809   3.64   0.99      12  0.063 **  2-fold h ( 1 0 0) {h,-k,-l}
  5   0.533   7.85   0.79     274  0.248 *   2-fold   ( 1-1 0) {-k,-h,-l}
  6   0.218   6.25   0.62     280  0.282     2-fold   ( 1 1 0) {k,h,-l}
  7   0.123   4.95   0.50     199  0.339     4-fold l ( 0 0 1) {-k,h,l}{k,-h,l}

so the 2-folds seem to be ok (even if the number of reflections compared is low in one case!), whereas the 4-fold symmetry is definitively not fulfilled.

At this point it is clear that the data are indeed orthorhombic although the metric symmetry is tetragonal.

Of particular note is the following pointless output:

Final point group choice has alternative indexing possibilities

Alternative indexing possibilities are marked '*' if the cells are 
  too different at the maximum resolution

    CellDifference(A) ReindexOperator
  1      0.0          [h,k,l]
  2      0.6          [-k,h,l]

which amounts to the same as what IDXREF prints when asked to index in space group 16:

 !!! WARNING !!! SOLUTION MAY NOT BE UNIQUE.
 OTHER POSSIBLE SOLUTIONS CAN BE TRIED IN THE "CORRECT" STEP
 BY SPECIFYING ALTERNATIVE SETS OF UNIT CELL BASIS VECTORS:

 UNIT_CELL_A-AXIS=    39.225    21.780    -7.264
 UNIT_CELL_B-AXIS=   -19.301    38.962    12.598
 UNIT_CELL_C-AXIS=    41.076   -26.084   143.608


 UNIT_CELL_A-AXIS=   -39.225   -21.780     7.264
 UNIT_CELL_B-AXIS=    19.301   -38.962   -12.598
 UNIT_CELL_C-AXIS=    41.076   -26.084   143.608

This means that one has to be particularly careful when merging data sets from crystals of this type because they may be indexed inconsistently.

Further investigation (using molecular replacement and refinement) resulted in the space group assigned to be P2(1), with 4 molecules in the ASU.