Table 3. Re-refinement and ensemble-refinement statistics for thrombin data sets.
| WT, Na+-bound | PPACK Cys | PPACK Ile | PPACK Thr | S195A | WT, Na+-free | E217K, Na+-free | D102N, Na+-free | |
|---|---|---|---|---|---|---|---|---|
| PDB code† | 3u69 | 3u8t | 3u8r | 3u8o | 1jou | 2afq | 1rd3 | 3bei |
| Resolution (Å) | 1.6 | 1.9 | 1.5 | 1.3 | 1.8 | 1.9 | 2.5 | 1.5 |
| phenix.refine re-refinement | ||||||||
| R work ‡ | 0.147 (0.135) | 0.141 (0.155) | 0.143 (0.131) | 0.145 (0.129) | 0.155 (0.222) | 0.148 (0.198) | 0.191 (0.229) | 0.156 (0.193) |
| R free ‡ | 0.165 (0.167) | 0.168 (0.195) | 0.163 (0.161) | 0.154 (0.149) | 0.170 (0.245) | 0.186 (0.229) | 0.236 (0.259) | 0.179 (0.215) |
| Geometric r.m.s.d. | ||||||||
| Bonds (Å) | 0.009 | 0.008 | 0.010 | 0.008 | 0.012 | 0.012 | 0.003 | 0.020 |
| Angles (°) | 1.28 | 1.24 | 1.36 | 1.34 | 1.36 | 1.347 | 0.79 | 1.76 |
| Dihedrals (°) | 16.3 | 13.7 | 14.2 | 13.6 | 14.2 | 14.0 | 13.9 | 15.4 |
| Ramachandran statistics (%) | ||||||||
| Outliers | 0.0 | 0.0 | 0.0 | 0.0 | 0.8 | 0.7 | 0.9 | 1.4 |
| Allowed | 3.4 | 3.6 | 2.8 | 3.6 | 3.4 | 2.9 | 6.3 | 3.2 |
| Favoured | 96.6 | 96.4 | 97.2 | 96.4 | 95.9 | 96.3 | 92.8 | 95.4 |
| phenix.ensemble_refinement | ||||||||
| τx (ps) | 0.8 | 0.6 | 0.9 | 1.2 | 0.6 | 0.6 | 0.3 | 0.9 |
| No. of models | 134 | 67 | 129 | 127 | 89 | 100 | 60 | 77 |
| R work | 0.124 | 0.123 | 0.122 | 0.114 | 0.140 | 0.139 | 0.174 | 0.140 |
| R free | 0.155 | 0.161 | 0.148 | 0.135 | 0.167 | 0.174 | 0.218 | 0.163 |
| Geometric r.m.s.d. (centroid distribution) | ||||||||
| Bonds (Å) | 0.008 | 0.009 | 0.008 | 0.009 | 0.010 | 0.010 | 0.012 | 0.011 |
| Angles (°) | 1.15 | 1.21 | 1.18 | 1.28 | 1.12 | 1.12 | 1.10 | 1.12 |
| Dihedrals (°) | 8.4 | 9.0 | 8.2 | 8.5 | 8.2 | 8.4 | 9.1 | 8.1 |
| Geometric r.m.s.d. (whole distribution) | ||||||||
| Bonds (Å) | 0.015 | 0.016 | 0.016 | 0.017 | 0.016 | 0.016 | 0.016 | 0.018 |
| Angles (°) | 1.93 | 1.79 | 1.96 | 2.07 | 1.79 | 1.77 | 1.69 | 2.04 |
| Dihedrals (°) | 20.2 | 18.0 | 18.8 | 18.5 | 18.8 | 18.5 | 19.7 | 19.1 |
| Ramachandran statistics (whole distribution) (%) | ||||||||
| Outliers | 2.8 | 1.6 | 2.0 | 1.3 | 3.3 | 3.3 | 4.1 | 3.7 |
| Allowed | 6.5 | 6.3 | 5.8 | 6.0 | 6.7 | 6.2 | 10.9 | 6.7 |
| Favoured | 90.7 | 92.1 | 92.1 | 92.7 | 89.8 | 90.5 | 85.8 | 89.4 |
| Ramachandran statistics (per torsion angle) (%) | ||||||||
| Outliers | 1. 5 | 1.5 | 0.4 | 0.4 | 1.0 | 2.0 | 1.2 | 3.5 |
| Allowed | 3.6 | 4.4 | 3.3 | 3.6 | 2.1 | 2.4 | 3.1 | 2.2 |
| Favoured | 94.9 | 94.1 | 96.4 | 96.0 | 97.0 | 95.6 | 95.6 | 94.4 |
†
References associated with the PDB files used in this table: 3u69, 3u8t, 3u8r and 3u8o, Figueiredo et al. (2012 ▶); 1jou, Huntington & Esmon (2003 ▶); 2afq, Johnson et al. (2005 ▶); 1rd3, Carter et al. (2004 ▶); 3bei, Gandhi et al. (2008 ▶).
‡
Values in parentheses are those reported in the original PDB entry.