Table 1. Data-collection and refinement statistics.
Values in parentheses are for the highest resolution shell.
| Crystal | Apo YfeA | Reconstituted holo YfeA |
|---|---|---|
| PDB code | 6q1c | 6q1d |
| Data collection | ||
| Wavelength (Å) | 1.28242 | 1.28232 |
| Space group | P212121 | P212121 |
| a, b, c (Å) | 40.0, 52.4, 113.3 | 39.9, 50.9, 115.5 |
| Resolution (Å) | 50.0–1.76 (1.79–1.76) | 50.0–1.79 (1.82–1.79) |
| Unique reflections | 24085 (1082) | 23030 (1135) |
| Completeness (%) | 98.5 (90.5) | 99.9 (99.9) |
| Multiplicity | 3.5 (2.5) | 6.7 (6.3) |
| CC1/2 | 92.3 (75.4) | 96.7 (97.3) |
| Overall CCanom † | 4.0 | 36.9 |
| R merge (%) | 8.5 (38.2) | 8.9 (42.8) |
| R meas (%) | 9.9 (48.0) | 9.7 (46.8) |
| R p.i.m. (%) | 5.0 (28.5) | 3.7 (18.7) |
| Mean I/σ(I) | 35.4 (2.0) | 43.1 (4.6) |
| Refinement | ||
| Resolution (Å) | 38.5–1.76 (1.78–1.76) | 46.6–1.79 (1.81–1.79) |
| No. of non-anomalous reflections | 24035 | 22885 |
| Completeness (%) | 94.6 (75.6) | 99.8 (98.7) |
| R work (%) | 19.0 (28.6) | 18.4 (25.3) |
| R free ‡ (%) | 23.9 (32.9) | 21.9 (26.8) |
| Wilson B factor (Å2) | 30.7 | 26.3 |
| Average B factors (Å2) | ||
| Overall | 35.9 | 31.2 |
| Protein atoms | 2042 | 2153 |
| Solvent atoms | 166 H2O | 158 H2O, 1 Zn |
| No. of molecules in ASU§ | 1 | 1 |
| R.m.s.d., bonds (Å) | 0.007 | 0.007 |
| R.m.s.d., angles (°) | 0.776 | 0.815 |
| Ramachandran plot | ||
| Favored (%) | 99.6 | 97.1 |
| Allowed (%) | 0.39 | 2.94 |
| Outliers (%) | 0 | 0 |
| Clashscore | 4.41 | 1.16 |
| MolProbity score | 1.22 | 0.99 |
| Model parameters | ||
| Average B factors (Å2) | ||
| His76 | 34.6 | 25.1 |
| His141 | 27.5 | 20.2 |
| Glu207 | 50.0 | 23.4 |
| Asp282 | 31.9 | 19.5 |
| Zinc | Not modeled | 27.2 |
| Occupancy | ||
| Zinc | Not modeled | 0.42 |
| Anomalous difference (σ) | ||
| Zinc | 5.6 | 66.6 |
†
Calculated by AIMLESS from the CCP4 suite.
‡
The test set uses ∼5% of data.
§
ASU, asymmetric unit.