Table 2. Re-refinement and ensemble-refinement statistics for FD data sets.
| Wild type | R202A | S183A | Triple mutant | Antibody-bound (form 1) | Antibody-bound (form 2) | |
|---|---|---|---|---|---|---|
| PDB code† | 1dsu | 4cbn | 2xw9 | 1dst | 4d9r | 4d9q |
| Resolution (Å) | 2.0 | 1.8 | 1.2 | 2.0 | 2.4 | 2.3 |
| phenix.refine re-refinement | ||||||
| R work ‡ | 0.149 (0.188) | 0.190 (N/A) | 0.156 (0.145) | 0.168 (0.193) | 0.194 (0.204) | 0.192 (0.184) |
| R free ‡ | 0.188 (0.203) | 0.219 (N/A) | 0.172 (0.176) | 0.200 (0.213) | 0.231 (0.245) | 0.220 (0.223) |
| Geometric r.m.s.d. | ||||||
| Bonds (Å) | 0.004 | 0.007 | 0.008 | 0.004 | 0.004 | 0.004 |
| Angles (°) | 0.82 | 1.24 | 1.33 | 0.96 | 0.87 | 0.85 |
| Dihedrals (°) | 12.8 | 15.4 | 13.3 | 12.2 | 14.2 | 12.9 |
| Ramachandran statistics (%) | ||||||
| Outliers | 0.2 | 1.3 | 0.4 | 0.9 | 0.2 | 0.0 |
| Allowed | 3.4 | 3.6 | 2.0 | 3.2 | 4.1 | 3.1 |
| Favoured | 96.3 | 95.2 | 97.6 | 95.9 | 95.7 | 96.9 |
| phenix.ensemble_refinement | ||||||
| τx (ps) | 0.5 | 0.6 | 1.4 | 0.5 | 1.0§ | 1.0§ |
| No. of models | 50 | 77 | 170 | 84 | 800 | 800 |
| R work | 0.117 | 0.166 | 0.125 | 0.142 | 0.183 | 0.182 |
| R free | 0.164 | 0.213 | 0.152 | 0.186 | 0.239 | 0.219 |
| Geometric r.m.s.d. (centroid distribution) | ||||||
| Bonds (Å) | 0.005 | 0.009 | 0.008 | 0.004 | 0.006 | 0.006 |
| Angles (°) | 0.87 | 1.12 | 1.15 | 0.75 | 1.04 | 0.931 |
| Dihedrals (°) | 8.0 | 8.6 | 7.6 | 7.0 | 9.2 | 9.14 |
| Geometric r.m.s.d. (whole distribution) | ||||||
| Bonds (Å) | 0.008 | 0.014 | 0.015 | 0.008 | 0.009 | 0.006 |
| Angles (°) | 1.27 | 1.78 | 1.95 | 1.23 | 1.08 | 1.05 |
| Dihedrals (°) | 16.7 | 17.6 | 16.9 | 16.7 | 16.2 | 15.6 |
| Ramachandran statistics (whole distribution) (%) | ||||||
| Outliers | 1.4 | 5.6 | 2.7 | 3.4 | 4.8 | 3.6 |
| Allowed | 6.0 | 8.6 | 5.7 | 8.6 | 10.3 | 8.3 |
| Favoured | 92.7 | 85.8 | 91.7 | 88.0 | 84.9 | 88.1 |
| Ramachandran statistics (per torsion angle) (%) | ||||||
| Outliers | 0.2 | 5.1 | 1.8 | 0.5 | 2.4 | 2.3 |
| Allowed | 3.0 | 4.6 | 2.2 | 4.3 | 4.2 | 3.5 |
| Favoured | 96.8 | 90.3 | 96.0 | 95.2 | 93.4 | 94.2 |
†
References associated with the PDB files used in this table: 1dsu, Narayana et al. (1994 ▶); 4cbn (refined with phenix.refine) and 4cbo (refined with phenix.ensemble_refinement), this work; 2xw9, Forneris et al. (2010 ▶); 1dst, Kim et al. (1995a ▶); 4d9r and 4d9q, Katschke et al. (2012 ▶).
‡
Values in parentheses are those reported in the original PDB entry.
§
For the two large FD–antibody structures determined at lower resolution, automatic default selection of τx yielded very short averaging windows; simulation of these structures were performed with τx set to 1.0 ps.