Old way of Space group determination
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Space group determination can be done within XDS by following these steps:
- an initial data reduction in P1, using SPACE_GROUP_NUMBER=0 (or even omitting that line)
- after CORRECT has thus run in P1, one may try other spacegroups by inspecting the table "DETERMINATION OF LATTICE CHARACTER AND BRAVAIS LATTICE" in IDXREF.LP (see the example below).
- for each possible lattice character, starting with the one corresponding to highest symmetry, do:
- look up space groups corresponding to lattice characters from the list BRAVAIS-TYPE / POSSIBLE SPACE-GROUPS FOR PROTEIN CRYSTALS in IDXREF.LP (repeated at bottom of this article).
- modify SPACE_GROUP_NUMBER=<number according to that list>
- modify or insert REIDX=<12 numbers corresponding to the lattice character, from the table>
- modify or insert UNIT_CELL_PARAMETERS= according to table, but make them obey space group requirements
- run XDS with JOB=CORRECT. Inspect CORRECT.LP and note R-factors, I/sigma and a and b modifiers of standard deviations
- repeat for each possible lattice character and finally decide on space group(s)
Example of table "DETERMINATION OF LATTICE CHARACTER AND BRAVAIS LATTICE":
LATTICE- BRAVAIS- QUALITY UNIT CELL CONSTANTS (ANGSTROEM & DEGREES) REINDEXING CARD (CORRECT)
CHARACTER LATTICE OF FIT a b c alpha beta gamma
1 cF 999.0 329.1 328.9 329.5 120.2 83.7 127.4 1 1 -1 0 1 -1 1 0 -1 -1 -1 0
2 hR 919.0 219.6 285.4 329.4 114.5 85.4 109.9 1 1 0 0 -1 0 -1 0 -1 1 1 0
3 cP 919.7 145.8 164.1 245.4 90.1 90.0 90.1 -1 0 0 0 0 1 0 0 0 0 -1 0
5 cI 999.0 285.4 219.4 294.9 65.5 44.4 70.3 -1 0 -1 0 -1 1 0 0 0 1 -1 0
4 hR 917.8 219.6 285.4 328.9 114.5 85.5 109.8 -1 -1 0 0 1 0 -1 0 1 -1 1 0
6 tI 999.0 294.9 285.4 219.4 70.3 65.5 44.4 0 1 -1 0 -1 0 -1 0 -1 1 0 0
7 tI 999.0 285.4 219.4 294.9 65.5 44.4 70.3 -1 0 -1 0 -1 1 0 0 0 1 -1 0
8 oI 999.0 219.4 285.4 294.9 44.4 65.5 70.3 1 -1 0 0 1 0 1 0 0 -1 1 0
9 hR 881.8 145.8 219.4 767.9 91.8 101.0 131.6 1 0 0 0 -1 1 0 0 -1 -1 3 0
10 mC 135.8 219.4 219.6 245.4 89.9 90.1 96.8 1 -1 0 0 1 1 0 0 0 0 1 0
11 tP 136.4 145.8 164.1 245.4 90.1 90.0 90.1 -1 0 0 0 0 1 0 0 0 0 -1 0
12 hP 385.3 145.8 164.1 245.4 90.1 90.0 90.1 -1 0 0 0 0 1 0 0 0 0 -1 0
13 oC 135.8 219.4 219.6 245.4 90.1 90.1 83.2 -1 1 0 0 1 1 0 0 0 0 -1 0
15 tI 632.0 145.8 164.1 537.2 72.3 74.3 90.1 -1 0 0 0 0 1 0 0 -1 1 -2 0
16 oF 999.0 219.4 219.6 537.2 92.7 114.0 83.2 1 -1 0 0 -1 -1 0 0 -1 1 -2 0
14 mC 135.2 219.4 219.6 245.4 90.1 90.1 83.2 -1 1 0 0 1 1 0 0 0 0 -1 0
17 mC 999.0 219.6 219.4 285.4 70.3 109.9 83.2 -1 -1 0 0 1 -1 0 0 1 0 1 0
18 tI 999.0 294.9 329.4 145.8 63.7 90.0 110.0 0 -1 1 0 1 -1 -1 0 1 0 0 0
19 oI 999.0 145.8 294.9 329.4 70.0 63.7 90.0 -1 0 0 0 0 -1 1 0 -1 1 1 0
20 mC 783.5 295.5 294.9 145.8 90.0 90.0 112.4 0 1 1 0 0 1 -1 0 -1 0 0 0
21 tP 785.1 164.1 245.4 145.8 90.0 90.1 90.1 0 1 0 0 0 0 -1 0 -1 0 0 0
22 hP 999.0 164.1 245.4 145.8 90.0 90.1 90.1 0 1 0 0 0 0 -1 0 -1 0 0 0
23 oC 783.2 294.9 295.5 145.8 90.0 90.0 67.6 0 1 -1 0 0 -1 -1 0 -1 0 0 0
24 hR 999.0 434.5 295.5 145.8 90.0 70.5 87.2 -1 2 -1 0 0 -1 -1 0 -1 0 0 0
25 mC 782.6 294.9 295.5 145.8 90.0 90.0 67.6 0 1 -1 0 0 -1 -1 0 -1 0 0 0
26 oF 623.1 145.8 359.0 512.0 83.3 106.6 113.9 1 0 0 0 -1 2 0 0 -1 0 2 0
27 mC 500.0 359.0 145.8 294.9 90.0 120.5 66.1 -1 2 0 0 -1 0 0 0 0 -1 1 0
28 mC 252.2 145.8 512.0 164.1 89.9 90.1 73.4 -1 0 0 0 -1 0 2 0 0 1 0 0
29 mC 251.8 145.8 359.0 245.4 89.9 90.0 66.1 1 0 0 0 1 -2 0 0 0 0 -1 0
30 mC 315.8 164.1 517.1 145.8 90.0 90.1 71.6 0 1 0 0 0 1 -2 0 -1 0 0 0
31 aP 0.3 145.8 164.1 245.4 89.9 90.0 89.9 1 0 0 0 0 1 0 0 0 0 1 0
32 oP 2.8 145.8 164.1 245.4 90.1 90.0 90.1 -1 0 0 0 0 1 0 0 0 0 -1 0
40 oC 315.8 164.1 517.1 145.8 90.0 90.1 108.4 0 -1 0 0 0 1 -2 0 1 0 0 0
35 mP 0.9 164.1 145.8 245.4 90.0 90.1 90.1 0 -1 0 0 1 0 0 0 0 0 1 0
36 oC 252.2 145.8 511.9 164.1 89.9 90.1 106.5 -1 0 0 0 1 0 2 0 0 1 0 0
33 mP 2.5 145.8 164.1 245.4 90.1 90.0 90.1 -1 0 0 0 0 1 0 0 0 0 -1 0
38 oC 251.6 145.8 359.0 245.4 89.9 90.0 113.9 1 0 0 0 -1 2 0 0 0 0 1 0
34 mP 2.2 145.8 245.4 164.1 90.1 90.1 90.0 1 0 0 0 0 0 1 0 0 -1 0 0
42 oI 565.2 145.8 164.1 537.2 107.7 105.7 90.1 1 0 0 0 0 -1 0 0 -1 1 -2 0
41 mC 315.5 517.1 164.1 145.8 90.1 90.0 71.6 0 -1 2 0 0 -1 0 0 1 0 0 0
37 mC 250.3 511.9 145.8 164.1 90.1 90.1 73.5 -1 0 -2 0 -1 0 0 0 0 1 0 0
39 mC 249.7 359.0 145.8 245.4 90.0 90.1 66.1 1 -2 0 0 1 0 0 0 0 0 1 0
43 mI 999.0 219.4 537.2 164.1 107.7 138.4 66.0 -1 1 0 0 -1 1 -2 0 0 -1 0 0
44 aP 0.0 145.8 164.1 245.4 90.1 90.0 90.1 -1 0 0 0 0 1 0 0 0 0 -1 0
This list is somewhat easier to go through by running sortlattices - the top 12 sorted by "Quality of Fit (QoF)" are:
44 aP 0.0 145.8 164.1 245.4 90.1 90.0 90.1 -1 0 0 0 0 1 0 0 0 0 -1 0 31 aP 0.3 145.8 164.1 245.4 89.9 90.0 89.9 1 0 0 0 0 1 0 0 0 0 1 0 35 mP 0.9 164.1 145.8 245.4 90.0 90.1 90.1 0 -1 0 0 1 0 0 0 0 0 1 0 34 mP 2.2 145.8 245.4 164.1 90.1 90.1 90.0 1 0 0 0 0 0 1 0 0 -1 0 0 33 mP 2.5 145.8 164.1 245.4 90.1 90.0 90.1 -1 0 0 0 0 1 0 0 0 0 -1 0 32 oP 2.8 145.8 164.1 245.4 90.1 90.0 90.1 -1 0 0 0 0 1 0 0 0 0 -1 0 14 mC 135.2 219.4 219.6 245.4 90.1 90.1 83.2 -1 1 0 0 1 1 0 0 0 0 -1 0 10 mC 135.8 219.4 219.6 245.4 89.9 90.1 96.8 1 -1 0 0 1 1 0 0 0 0 1 0 13 oC 135.8 219.4 219.6 245.4 90.1 90.1 83.2 -1 1 0 0 1 1 0 0 0 0 -1 0 11 tP 136.4 145.8 164.1 245.4 90.1 90.0 90.1 -1 0 0 0 0 1 0 0 0 0 -1 0 39 mC 249.7 359.0 145.8 245.4 90.0 90.1 66.1 1 -2 0 0 1 0 0 0 0 0 1 0 37 mC 250.3 511.9 145.8 164.1 90.1 90.1 73.5 -1 0 -2 0 -1 0 0 0 0 1 0 0
Obviously there's a sharp increase from Lattice character 32 (QoF=2.8) to 14 (QoF=135.2) indicating that the highest symmetry spacegroups consistent with the observed pattern of Bragg reflections are oP (orthorhombic primitive).
BRAVAIS- POSSIBLE SPACE-GROUPS FOR PROTEIN CRYSTALS
TYPE [SPACE GROUP NUMBER,SYMBOL]
aP [1,P1]
mP [3,P2] [4,P2(1)]
mC,mI [5,C2]
oP [16,P222] [17,P222(1)] [18,P2(1)2(1)2] [19,P2(1)2(1)2(1)]
oC [21,C222] [20,C222(1)]
oF [22,F222]
oI [23,I222] [24,I2(1)2(1)2(1)]
tP [75,P4] [76,P4(1)] [77,P4(2)] [78,P4(3)] [89,P422] [90,P42(1)2]
[91,P4(1)22] [92,P4(1)2(1)2] [93,P4(2)22] [94,P4(2)2(1)2]
[95,P4(3)22] [96,P4(3)2(1)2]
tI [79,I4] [80,I4(1)] [97,I422] [98,I4(1)22]
hP [143,P3] [144,P3(1)] [145,P3(2)] [149,P312] [150,P321] [151,P3(1)12]
[152,P3(1)21] [153,P3(2)12] [154,P3(2)21] [168,P6] [169,P6(1)]
[170,P6(5)] [171,P6(2)] [172,P6(4)] [173,P6(3)] [177,P622]
[178,P6(1)22] [179,P6(5)22] [180,P6(2)22] [181,P6(4)22] [182,P6(3)22]
hR [146,R3] [155,R32]
cP [195,P23] [198,P2(1)3] [207,P432] [208,P4(2)32] [212,P4(3)32]
[213,P4(1)32]
cF [196,F23] [209,F432] [210,F4(1)32]
cI [197,I23] [199,I2(1)3] [211,I432] [214,I4(1)32]