Trypsin inhibitor ACA2014: Difference between revisions
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These data (courtesy Alex Wlodawer) were collected at Argonne on Nov 8, 2013 . Data are at | These data (courtesy Alex Wlodawer) were collected at Argonne on Nov 8, 2013 . Data are at https://{{SERVERNAME}}/pub/datasets/ACA2014_Trypsin_with_inhibitor/ . | ||
IDXREF result: | IDXREF result: | ||
| Line 182: | Line 182: | ||
This means that one has to be particularly careful when merging data sets from crystals of this type because they may be indexed inconsistently. | 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. | |||
Latest revision as of 19:24, 24 March 2020
These data (courtesy Alex Wlodawer) were collected at Argonne on Nov 8, 2013 . Data are at https://wiki.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.