Table 1.
X-ray diffraction and crystal structure refinement statistics for DNMT3B–3L and DNMT3B–3L–DNA complexes
| DNMT3B–3L–DNA (CpGpG) | DNMT3B–3L–DNA (CpGpT) | DNMT3B–3L (i) | DNMT3B–3L (ii) | DNMT3B (Q772R)–3L | |
|---|---|---|---|---|---|
| PDB entry | 6KDA | 6KDB | 6KDL | 6KDP | 6KDT |
| Data collection | |||||
| Space group | P31 | P31 | P31 | C2221 | C2221 |
| Cell dimensions | |||||
| a, b, c (Å) | 193.87, 193.87, 49.74 | 194.82, 194.82, 49.84 | 192.93, 192.93, 50.04 | 72.10, 234.06, 230.95 | 60.35, 240.78, 232.13 |
| α, β, γ (°) | 90, 90, 120 | 90, 90, 120 | 90, 90, 120 | 90, 90, 90 | 90, 90, 90 |
| Resolution (Å)a | 30–2.91 | 30–2.85 | 30–3.27 | 30–2.94 | 30–2.85 |
| (3.01–2.91)a | (2.95–2.85)a | (3.39–3.27)a | (3.04–2.94)a | (2.95–2.85)a | |
| R merge | 0.061 (0.745) | 0.047 (0.524) | 0.052 (0.446) | 0.100 (0.538) | 0.127 (0.734) |
| CC1/2 | 0.972 (0.852) | 0.965 (0.807) | 0.957 (0.883) | 0.989 (0.962) | 0.955 (0.824) |
| I/σI | 25.95 (2.05) | 29.05 (1.51) | 17.61 (2.05) | 19.19 (3.15) | 13.24 (2.54) |
| Completeness (%) | 100 (99.8) | 99.2 (92.1) | 98.8 (99.3) | 98.0 (90.3) | 97.1 (97.9) |
| Redundancy | 4.8 (4.2) | 4.5 (3.0) | 2.7 (2.4) | 5.9 (5.0) | 5.2 (5.5) |
| Refinement | |||||
| Resolution (Å) | 29.5–2.91 | 29.61–2.85 | 27.79–3.27 | 29.80–2.94 | 27.37–2.87 |
| No. of reflections | 42 169 | 43 939 | 28 669 | 32 943 | 36 770 |
| R work | 0.1746 (0.2518) | 0.1629 (0.2283) | 0.1790 (0.2339) | 0.2050 (0.2717) | 0.1938 (0.2943) |
| R free | 0.2130 (0.3073) | 0.2005 (0.2984) | 0.2121 (0.3044) | 0.2440 (0.3232) | 0.2422 (0.3620) |
| No. of atoms | |||||
| Macromolecules | 8699 | 8700 | 7460 | 7721 | 7729 |
| Water | 305 | 316 | 190 | 111 | 160 |
| B-factors (Å2) | |||||
| Protein | 75.57 | 82.39 | 89.18 | 56.89 | 56.15 |
| DNA | 167.00 | 219.19 | |||
| Cofactor (SAH) | 27.17 | 38.16 | 67.03 | 39.24 | 57.52 |
| Water | 43.95 | 54.63 | 45.00 | 38.28 | 45.27 |
| RMSDb | |||||
| Bond lengths (Å) | 0.015 | 0.009 | 0.003 | 0.004 | 0.009 |
| Bond angles (°) | 1.34 | 1.11 | 0.64 | 0.64 | 1.00 |
| Ramachandran | |||||
| Favored (%) | 93.69 | 95.22 | 95.83 | 96.53 | 96.22 |
| Allowed (%) | 6.31 | 4.78 | 4.17 | 3.47 | 3.78 |
| Disallowed (%) | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |
aStatistics for the highest resolution shell are shown in parentheses.
bCategories were defined using PHENIX.