Table 2. Structure-refinement and validation statistics.
| Data set | EP–29 | EP–30 | EP–39 | EP–42 | EP–50 | EP–51 | EP–53 | EP–91 | EP–97 |
|---|---|---|---|---|---|---|---|---|---|
| Refinement program | PHENIX v.1.9-1692 | ||||||||
| Resolution limits (Å) | 42.7–1.10 | 39.4–1.31 | 42.7–1.17 | 34.7–1.35 | 39.6–1.25 | 42.8–1.27 | 42.7–1.44 | 34.8–1.28 | 42.7–1.03 |
| Completeness (%) | 96.9 | 99.5 | 98.8 | 99.1 | 99.7 | 99.8 | 97.9 | 99.8 | 93.6 |
| Data cutoff [F/σ(F)] | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| No. of reflections | |||||||||
| Working set | 118847 | 74055 | 101857 | 67321 | 85676 | 80559 | 54387 | 80309 | 141365 |
| Test set | 6255 | 3898 | 5360 | 3543 | 4510 | 4240 | 2862 | 2099 | 7440 |
| R work (%) | 11.45 | 12.75 | 11.46 | 11.68 | 11.27 | 11.58 | 12.01 | 13.80 | 10.99 |
| R free (%) | 12.97 | 15.83 | 13.87 | 14.16 | 14.02 | 14.49 | 15.91 | 16.40 | 12.55 |
| DPI† (Å) | 0.029 | 0.055 | 0.034 | 0.057 | 0.041 | 0.046 | 0.080 | 0.029 | 0.023 |
| No. of atoms | |||||||||
| Total | 2876 | 2763 | 2860 | 2856 | 2838 | 2887 | 2851 | 2889 | 2950 |
| Protein | 2470 | 2459 | 2472 | 2468 | 2464 | 2458 | 2459 | 2473 | 2488 |
| Fragment | 13 | 12 | 10 | 8 | 12 | 28 | 12 | 16 | 12 |
| Other ligands | 64 | 66 | 74 | 54 | 54 | 48 | 50 | 92 | 54 |
| Waters | 329 | 226 | 304 | 326 | 308 | 353 | 330 | 308 | 396 |
| R.m.s. deviations | |||||||||
| Bonds (Å) | 0.007 | 0.007 | 0.007 | 0.009 | 0.010 | 0.007 | 0.008 | 0.006 | 0.006 |
| Angles (°) | 1.3 | 1.2 | 1.2 | 1.3 | 1.4 | 1.2 | 1.3 | 1.2 | 1.3 |
| Average B factors (Å2) | |||||||||
| Protein | 11.8 | 13.9 | 12.6 | 12.8 | 13.3 | 12.8 | 14.8 | 13.0 | 12.2 |
| Fragment | 21.4 | 13.3 | 23.4 | 25.1 | 16.8 | 34.2 | 20.8 | 21.1 | 16.0 |
| Other ligands | 39.8 | 37.7 | 35.1 | 34.4 | 34.4 | 34.5 | 34.9 | 40.5 | 31.2 |
| Waters | 28.2 | 29.3 | 28.9 | 27.9 | 31.7 | 28.7 | 30.1 | 28.4 | 29.0 |
| Ramachandran plot | |||||||||
| Outliers (%) | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.06 | 0.0 |
| Allowed (%) | 1.4 | 1.7 | 1.4 | 1.7 | 1.7 | 1.7 | 2.0 | 1.4 | 1.7 |
| Favoured (%) | 98.6 | 98.3 | 98.6 | 98.3 | 98.3 | 98.3 | 98.0 | 98.6 | 98.3 |
| PDB code | 4y38 | 4y3j | 4ze6 | 4y3y | 4y48 | 4y4d | 4y4g | 4zea | 4y4j |
DPI was calculated using the Online_DPI server (Kumar et al., 2015 ▸).