Table 2.
Refinement statistics for PmDAP IV.
| Data set | Free | Inhibitor-1c | Ile-Pro | Lys-Pro |
|---|---|---|---|---|
| PDB ID | 5YP1 | 5YP2 | 5YP3 | 5YP4 |
| Resolution range (Å) | 40.00–2.47 | 40.00–2.13 | 40.00–2.44 | 40.00–1.90 |
| Completeness (%) | 99.78 | 99.23 | 97.21 | 94.17 |
| No. of reflections | ||||
| working set test set |
119,191 6,289 |
89,236 4,652 |
130,819 6,835 |
232,846 12,222 |
| R-factor | 0.218 | 0.178 | 0.238 | 0.164 |
| Free R-factor | 0.284 | 0.226 | 0.286 | 0.213 |
| No. of protein atoms (avg. B-factors (Å2)) |
22,059 (45.4) |
11,320 (32.5) |
22,640 (44.4) |
22,270 (22.2) |
| No. of ligand atoms (avg. B-factors (Å2)) |
— | 40 (2 × 20) (24.5) |
60 (4 × 15) (25.7) |
65 (3 × 16 + 1 × 17) (20.7) |
| No. of glycerol atoms (avg. B-factors (Å2)) |
6 (1 × 6) (48.0) |
18 (3 × 6) (46.0) |
6 (1 × 6) (52.3) |
126 (21 × 6) (39.2) |
| No. of water molecules (avg. B-factors (Å2)) |
598 (33.6) |
700 (33.5) |
452 (31.3) |
2,877 (31.3) |
| Ramachandran plot statistics | ||||
| favored (%) allowed (%) outlier (%) |
2,617 (93.2) 164 (5.8) 27 (1.0) |
1,392 (96.4) 52 (3.6) 0 (0.0) |
2,710 (93.8) 172 (6.0) 6 (0.2) |
2,747 (97.1) 82 (2.9) 0 (0.0) |
| RMSD | ||||
| bonds (Å) angles (°) |
0.01 1.70 |
0.02 1.84 |
0.01 1.77 |
0.02 1.90 |