Table 1. Data collection and refinement statistics.
| KDM4B-DTD apo form | KDM4A-DTD H3K23me3 | KDM4A-DTD apo form 1 | KDM4A-DTD apo form 2 | |
|---|---|---|---|---|
| Data collection | ||||
| Space group | P 31 | P 32 | R 32:h | I213 |
| Cell dimensions | ||||
| a, b, c (Å) | 77.4, 77.4, 50.8 | 106.2, 106.2, 79.2 | 190.6, 190.6, 117.0 | 134.8, 134.8, 134.8 |
| α, β, γ (°) | 90.0, 90.0, 120.0 | 90.0, 90.0, 120.0 | 90.0, 90.0, 120.0 | 90.0, 90.0, 90.0 |
| Resolution (Å) | 30–2.56 (2.68–2.56) | 30–2.28 (2.32–2.28) | 36–1.99 (2.01–1.99) | 42–2.15 (2.28–2.15) |
| Rmerge | 0.120 (0.797) | 0.225 (1.885) | 0.130 (1.158) | 0.076 (0.523) |
| I/σI | 6.73 (2.28) | 12.95 (1.42) | 12.6 (2.35) | 25.1 (5.74) |
| Completeness (%) | 100.0 (100.0) | 100.0 (100.0) | 100.0 (100.0) | 100.0 (100.0) |
| Redundancy | 6.6 (6.3) | 11.3 (8.7) | 9.8 (9.7) | 13.8 (13.8) |
| CC1/2 | 0.99 (0.74) | 0.99 (0.46) | 0.99 (0.67) | 0.99 (0.95) |
| Refinement | ||||
| Resolution (Å) | 30–2.56 | 30–2.28 | 36–1.99 | 42–2.15 |
| No. reflections | 71,716 | 466,599 | 542,229 | 306,479 |
| Rwork/Rfree | 0.197/0.254 | 0.264/0.295 | 0.168/0.195 | 0.159/0.199 |
| Peptide RSCC* | — | 0.92 | — | — |
| No. atoms (non-H) | ||||
| Protein | 1,716 | 5,069 | 3,795 | 1,974 |
| Peptide | — | 248 | — | — |
| Water | 66 | 216 | 515 | 242 |
| B-factors | ||||
| Protein | 48.2 | 42.0†/99.1‡ | 39.6 | 34.9 |
| Peptide | — | 46.0 | — | — |
| Water | 44.7 | 48.3 | 53.0 | 50.2 |
| Root mean squared deviations | ||||
| Bond lengths (Å) | 0.009 | 0.011 | 0.008 | 0.008 |
| Bond angles (°) | 1.12 | 1.39 | 1.10 | 1.11 |
| PDB code | 4UC4 | 5D6Y | 5D6W | 5D6X |
*RSCC is the real-space correlation to electron density calculated by phenix.
†Average B-factor of ordered chains A–D in asymmetric unit.
‡Average B-factor of disordered chains E–F in asymmetric unit.