Table 1.
Crystallographic data collection and refinement statistics of NDM-1 in complex with hydrolyzed imipenem
| Crystal 1 | Crystal 2 | Crystal 3 | Crystal 4 | Crystal 5 | Crystal 6 | |
|---|---|---|---|---|---|---|
| Data collection | ||||||
| Space group | P2 1 | P2 1 | P2 1 2 1 2 1 | P2 1 2 1 2 1 | P2 1 | P2 1 2 1 2 1 |
| Cell dimensions | ||||||
| a, b, c (Å) | 69.24, 73.61, 154.52 | 69.38, 74.10, 154.52 | 69.35, 73.93, 77.49 | 69.77, 74.01, 77.43 | 69.90, 74.10, 155.63 | 69.22, 73.76, 77.43 |
| α, β, γ (°) | 90, 90.083, 90 | 90, 90.259, 90 | 90, 90, 90 | 90, 90, 90 | 90, 90.321, 90 | 90, 90, 90 |
| Resolution (Å)a | 2.0 (2.05–2.0) | 2.3 (2.36–2.30) | 1.95 (2.0–1.95) | 2.0 (2.05–2.0) | 2.0 (2.05–2.0) | 1.8 (1.84–1.8) |
| R sym a | 0.072 (0.440) | 0.080 (0.457) | 0.052 (0.244) | 0.085 (0.592) | 0.111 (0.593) | 0.070 (0.555) |
| I/σ(I)a | 8.65 (2.06) | 8.32 (2.06) | 15.06 (3.17) | 11.21 (2.70) | 7.10 (2.14) | 16.80 (2.55) |
| Completeness (%)a | 90.0 (61.6) | 95.2 (97.3) | 94.1 (70.4) | 99.8 (99.8) | 96.4 (98.8) | 94.0 (64.8) |
| Redundancya | 1.73 (1.37) | 1.94 (2.00) | 3.45 (2.19) | 3.80 (3.82) | 2.43 (2.43) | 6.36 (4.44) |
| Refinement | ||||||
| Resolution (Å) | 47.96–2.0 | 48.17–2.3 | 42.36–1.95 | 42.46–2.0 | 48.48–2.0 | 42.28–1.8 |
| Reflections | 100,028 | 69,446 | 28,575 | 27,718 | 105,994 | 35,229 |
| R work/R free | 0.1858/0.2285 | 0.1779/0.2372 | 0.1695/0.2172 | 0.1994/0.2344 | 0.2025/0.2342 | 0.1685/0.2038 |
| No. atoms | ||||||
| Protein | 13,600 | 13,592 | 3398 | 3387 | 13,600 | 3406 |
| Ligand | 168 | 168 | 42 | 42 | 216 | 42 |
| Water/Ion | 1954 | 1860 | 317 | 339 | 1871 | 377 |
| B-factors | ||||||
| Protein | 25.44 | 37.56 | 29.23 | 41.07 | 27.29 | 28.07 |
| Ligand | 35.44 | 49.65 | 46.11 | 47.7 | 34.81 | 45.46 |
| Water/Ion | 35.51 | 41.56 | 37.97 | 42.98 | 37.54 | 38.63 |
| R.m.s. deviations | ||||||
| Bond lengths (Å) | 0.005 | 0.004 | 0.004 | 0.005 | 0.006 | 0.008 |
| Bond angles (°) | 0.905 | 0.849 | 0.877 | 0.965 | 1.013 | 1.134 |
| Ramachandran plot | ||||||
| Favored (%) | 98.4 | 98.67 | 98.89 | 96.23 | 97.73 | 99.12 |
| Allowed (%) | 1.6 | 1.33 | 1.11 | 3.1 | 2.1 | 0.88 |
| Disallowed (%) | 0 | 0 | 0 | 0.67 | 0.17 | 0 |
| Captured complex | EI2 (Δ1) | EI1 (Δ2) | EP (Δ1) | EI2 (Δ1) | EI2 (Δ1) | EP (Δ1) |
| PDB ID | 5YPK | 5YPI | 5YPL | |||
aValues in parentheses are for highest-resolution shell