Table 2. Crystal properties and refinement statistics for inhibitors 1–5 bound to pcDHFR and hDHFR as NADPH ternary complexes.
Values in parentheses are for the highest resolution shells.
| pcDHFR–1 | pcDHFR–2 | pcDHFR–3 | pcDHFR–4 | pcDHFR–5 | hDHFR–3 | |
|---|---|---|---|---|---|---|
| PDB code | 3nz6 | 3nz9 | 3nza | 3nzb | 3nzc | 3nzd |
| Space group | P21 | P21 | P21 | P21 | P21 | H3 |
| Unit-cell parameters | ||||||
| a (Å) | 37.1 | 36.9 | 36.9 | 36.9 | 36.9 | 84.6 |
| b (Å) | 42.8 | 42.7 | 42.7 | 42.7 | 42.7 | 84.6 |
| c (Å) | 60.8 | 60.1 | 60.6 | 60.6 | 59.9 | 77.6 |
| β (°) | 94.4 | 94.8 | 94.6 | 94.6 | 94.8 | |
| Beamline | SSRL 11-1 | SSRL 11-1 | SSRL 11-1 | SSRL 11-1 | SSRL 11-1 | SSRL 9-2 |
| Resolution | 1.80 (1.86–1.80) | 1.60 (1.66–1.60) | 1.70 (1.76–1.70) | 1.30 (1.37–1.30) | 1.80 (1.86–1.80) | 1.80 (1.90–1.80) |
| Wavelength (Å) | 0.975 | 0.975 | 0.975 | 0.975 | 0.975 | 0.975 |
| Rmerge | 0.070 (0.58) | 0.028 (0.33) | 0.070 (0.38) | 0.046 (0.46) | 0.060 (0.34) | 0.062 (0.34) |
| Completeness (%) | 96.3 (98.8) | 96.6 (90.3) | 97.8 (98.0) | 87.5 (47.3) | 95.8 (83.8) | 95.3 (74.2) |
| Observed reflections | 17172 | 46806 | 21070 | 154924 | 17462 | 67454 |
| Unique reflections | 12344 | 24011 | 19449 | 44341 | 16720 | 18315 |
| 〈I/σ(I)〉 | 14.4 (0.58) | 13.1 (5.0) | 14.4 (4.4) | 12.8 (1.7) | 4.9 (0.5) | 15.0 (3.3) |
| Multiplicity | 3.7 (1.2) | 3.6 (3.2) | 2.5 (2.0) | 3.4 (2.1) | 3.5 (3.0) | 3.7 (3.2) |
| Resolution range | 32.7–2.0 (2.1–2.0) | 24.5–1.6 (1.7–1.6) | 27.8–1.8 (1.9–1.8) | 24.7–1.4 (1.5–1.4) | 32.5–1.9 (2.0–1.9) | 53.3–1.8 (1.9–1.8) |
| Reflections used | 11724 | 16107 | 13884 | 30117 | 11845 | 17366 |
| R factor | 0.21 | 0.20 | 0.21 | 0.24 | 0.21 | 0.16 |
| Rfree | 0.28 | 0.27 | 0.28 | 0.29 | 0.27 | 0.23 |
| Total protein/ligand atoms | 1931 | 1879 | 1893 | 1892 | 1782 | 1878 |
| Total waters | 166 | 114 | 116 | 73 | 48 | 296 |
| Average B factor (Å2) | 32.0 | 30.0 | 29.3 | 25.4 | 41.3 | 19.6 |
| Error in Luzzati plot | 0.29 | 0.21 | 0.23 | 0.21 | 0.25 | 0.17 |
| R.m.s. deviation from ideal | ||||||
| Bond lengths (Å) | 0.019 | 0.023 | 0.022 | 0.022 | 0.022 | 0.025 |
| Bond angles (°) | 2.11 | 2.34 | 2.00 | 2.02 | 1.98 | 2.23 |
| Ramachandran plot (%) | ||||||
| Most favored | 91.2 | 94.6 | 92.1 | 93.6 | 89.2 | 96.7 |
| Additional | 5.4 | 3.4 | 4.0 | 3.9 | 7.8 | 2.7 |
| Disallowed | 3.4 | 1.5 | 4.0 | 2.5 | 2.9 | 0.5 |
| Missing density† | 1–4, 83–89 | 1, 4, 83–89 | 1–4, 83–89 | 1–4, 83–89 | 1–4, 83–89 | |
†
Residues without interpretable density and not refined.