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Table 1: Summary of X-Ray diffraction data
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EHMT1 + AdoHcy |
EHMT1 + AdoHcy + H3K9me2 |
EHMT1 + AdoHcy + H3K9me |
EHMT2 + AdoHcy |
SUV39H2 + AdoMet |
PRDM2 |
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PDB Code |
2IGQ |
2RFI |
3HNA |
2O8J |
2R3A |
2QPW |
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Data Collection |
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X-ray source |
NSLS-X25 |
APS-17ID |
APS-17ID |
APS-17ID |
Rigaku FR-E |
CHESS-A1 |
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Space group |
P21 21 21 |
P21 21 21 |
P21 21 21 |
P1 |
P1 21 1 |
P21 21 21 |
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Cell dimensions |
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a, b, c (Å) |
74.52, 95.86, 102.12 |
84.59, 85.63, 95.67 |
83.53, 83.37, 95.13 |
56.59, 70.96, 83.05 |
45.75, 63.92, 64.53 |
36.46, 51.20, 70.89 |
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α, β, γ (°) |
90.00, 90.00, 90.00 |
90.00, 90.00, 90.00 |
90.00, 90.00, 90.00 |
81.11, 75.13, 88.39 |
90.00, 109.33, 90.00 |
90.00, 90.00, 90.00 |
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Resolution (Å) (highest resolution shell) |
69.84-2.00 (2.07-2.00) |
42.80-1.60 (1.64-1.60) |
62.75-1.50(1.58-1.50) |
79.30-1.80 (1.86-1.80) |
50.00-2.00 (2.08-2.00) |
50.00-1.79 (1.86-1.79) |
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Unique reflections |
44160 |
89676 |
106827 |
100323 |
22956 |
23999 |
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Rsym |
9.6 |
8.0 |
9.8 |
4.8 |
8.4 |
6.3 |
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I/σI |
8.8(1.3) |
10.8 (1.4) |
15.2(4.3) |
13.7(3.0) |
15.0(3.4) |
34.3 (6.0) |
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Completeness (%) |
92.6(83.2) |
96.5 (67.2) |
100.0(100.0) |
92.3(72.7) |
96.6 (92.9) |
99.7 (99.3) |
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Redundancy |
3.7(2.0) |
7.4 (3.0) |
8.2(8.2) |
3.2(3.2) |
2.4 (2.3) |
7.2 (6.4) |
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Refinement |
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Resolution (Å) |
42.11-2.00 |
42.80-1.59 |
62.75-1.50 |
79.31-1.80 |
35.38-2.00 |
41.49-1.79 |
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No. reflections (test set) |
44160 (2365) |
85102 (4475) |
101405 (5324) |
100323 (5287) |
21763 (1182) |
13205 (841) |
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Rwork/ Rfree (%) |
19.1/23.7 |
19.4/22.0 |
16.7/19.3 |
18.4/22.1 |
17.9/21.3 |
17.1/22.2 |
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No. atoms |
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Protein |
4084 |
4322 |
4550 |
8331 |
2154 |
1192 |
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Cofactor |
60 |
60 |
60 |
120 |
31 |
N/A |
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Water |
566 |
681 |
888 |
1780 |
254 |
145 |
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B-factors (Å2) |
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Protein |
31.7 |
24.8 |
15.1 |
24.2 |
29.2 |
21.8 |
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Cofactor |
44.5 |
33.2 |
13.1 |
24.3 |
25.7 |
N/A |
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Water |
40.4 |
32.6 |
31.9 |
32.8 |
38.3 |
36.2 |
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R.m.s deviations |
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Bond lengths (Å) |
0.015 |
0.009 |
0.009 |
0.013 |
0.017 |
0.019 |
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Bond angles (°) |
1.53 |
1.17 |
1.28 |
1.35 |
1.55 |
1.51 |
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Ramachandran plot % residues |
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Favored |
82.9 |
85.0 |
85.1 |
86.4 |
86.7 |
87.8 |
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Additionally allowed |
16.2 |
14.1 |
14.3 |
13.2 |
13.3 |
12.2 |
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Generously allowed |
0.5 |
0.4 |
0.2 |
0 |
0 |
0 |
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Disallowed |
0.5 |
0.4 |
0.4 |
0.4 |
0 |
0 |
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