Table 2. Refinement and model quality.
Values in parentheses are for the highest resolution shell.
| Crystal 1 | Crystal 2 | Crystal 3 | |
|---|---|---|---|
| R factor (%) | 15.90 (19.76) | 14.60 (20.57) | 15.92 (23.32) |
| R free † (%) | 20.21 (23.92) | 15.94 (24.36) | 20.07 (27.03) |
| No. of atoms | |||
| Total | 3074 | 3284 | 3227 |
| Macromolecules | 1475 | 1494 | 1476 |
| Ligands | 19 | 36 | 29 |
| Water | 111 | 205 | 222 |
| No. of protein residues | 185 | 187 | 187 |
| R.m.s.d., bonds (Å) | 0.012 | 0.009 | 0.010 |
| R.m.s.d., angles (°) | 1.34 | 1.29 | 1.27 |
| Ramachandran favoured (%) | 98 | 99 | 99 |
| Ramachandran outliers (%) | 0 | 0 | 0 |
| MolProbity clashscore | 5.4 | 1.32 | 3.67 |
| Percentile‡ | 96th [N = 743, 1.922 ± 0.25 Å] | 99th [N = 453, 1.395 ± 0.25 Å] | 97th [N = 819, 1.700 ± 0.25 Å] |
| MolProbity overall score | 1.29 | 0.85 | 1.16 |
| Percentile‡ | 99th [N = 11840, 1.922 ± 0.25 Å] | 100th [N = 3078, 1.395 ± 0.25 Å] | 99th [N = 9248, 1.700 ± 0.25 Å] |
| Average B factor (Å2) | |||
| Protein | 20.7 | 17.6 | 17.7 |
| Ligand | 45.3 | 24.1 | 41.1 |
| Solvent | 27.7 | 28.7 | 26.8 |
†
R free was calculated with 5% of the data set.
‡
The 100th percentile is the best among structures of comparable resolution; the 0th percentile is the worst. For the MolProbity clashscore the comparative set of structures was selected in 2004; that for the MolProbity score was selected in 2006.