Table 4. Structure-solution and refinement statistics.
Values in parentheses are for the outer shell.
| Apo BoSDR (PDB entry 5er6) | BoSDR–NAD+(PDB entry 5ha5) | |
|---|---|---|
| Resolution range (Å) | 50.00–1.55 (1.59–1.55) | 50.00–1.90 (1.95–1.90) |
| Completeness (%) | 98.3 | 99.9 |
| σ Cutoff | 3.0 | 3.0 |
| No. of reflections, working set | 135447 | 78757 |
| No. of reflections, test set | 2000 | 2005 |
| Final Rcryst | 0.146 (0.214) | 0.1519 (0.199) |
| Final Rfree | 0.167 (0.233) | 0.190 (0.218) |
| No. of non-H atoms | ||
| Protein | 6882 | 6901 |
| Coenzyme (NAD+) | 0 | 176 |
| IMD | 0 | 25 |
| EDO | 24 | 59 |
| ACT | 24 | 0 |
| Water | 1135 | 711 |
| Total | 8073 | 7868 |
| R.m.s. deviations | ||
| Bond lengths (Å) | 0.006 | 0.007 |
| Angles (°) | 11 | 16 |
| Average B factors (Å2) | ||
| Protein | 15 | 23 |
| Coenzyme (NAD+) | N.A.† | 26 |
| Other | 36 [EDO, ACT] | 47 [EDO, IMD] |
| Water | 32 | 35 |
| Overall | 18 | 24 |
| Ramachandran plot‡ | ||
| Most favored (%) | 98 | 97 |
| Allowed (%) | 2 | 2 |
†
N.A., not applicable.
‡
Based on MolProbity (Williams et al., 2018 ▸).