Table 1.
Crystallographic Data Collection and Refinement Statistics
| PDB Entry | VapXD (Selenomethionine) 6ZN8 | VapD (Wild Type) 6ZI0 | VapD (D7N) 6ZI1 |
|---|---|---|---|
| Data Collection | |||
| Wavelength (Å) | 0.979 | 0.98021 | 0.98021 |
| Resolution range | 46.88–3.21 (3.33–3.21)a | 85.88–2.50 (2.56–2.50) | 42.19–2.20(2.26–2.20) |
| Space group | I4132 | P6322 | P321 |
| Unit cell dimensions | |||
| a, b, c (Å) | 256.75, 256.75, 256.75 | 99.168, 99.168, 44.486 | 84.380, 84.380, 49.476 |
| α, β, γ (°) | 90, 90, 90 | 90, 90, 120 | 90, 90, 120 |
| Total no. of reflections | 172,895 (17,802) | 49,715(3,673) | 34,356 (2,279) |
| Unique reflections | 23,771 (2,337) | 4,800 (344) | 10,306 (736) |
| Multiplicity | 7.3 (7.6) | 10.3(10.7) | 3.3 (3.1) |
| Completeness (%) | 99.7 (99.7) | 99.9(100.0) | 97.2 (97.9) |
| Rmerge | 0.169 (1.37) | 0.212 (1.581) | 0.060 (0.928) |
| I/σ (I) | 9.2 (1.3) | 9.5 (1.3) | 12.1 (1.3) |
| CC1/2 | 0.99 (0.53) | 0.996 (0.55) | 0.999(0.61) |
| Refinement | |||
| Average B factor (Å2) | 100.7 | 76.2 | 58.9 |
| No. of reflections | 23,774 (2,337) | 4,560 (326) | 9,282 (668) |
| No. of reflections (free) | 2,351 (209) | 241 (18) | 1,028 (68) |
| Rwork (%) | 25.8 (34.9) | 22.0 (28.4) | 21.4(38.6) |
| Rfree (%) | 29.9 (39.6) | 26.4 (28.9) | 26.7 (40.9) |
| No. of atoms | |||
| Protein | 3,939 | 722 | 1,333 |
| Solvent | 0 | 55 | 88 |
| Ligand | 0 | 0 | 0 |
| RMSD bonds (Å) | 0.010 | 0.008 | 0.007 |
| RMSD angles (°) | 1.11 | 1.74 | 1.48 |
| Ramachandran statistics | |||
| favored (%) | 93.7 | 91.6 | 84.8 |
| Allowed (%) | 6.3 | 7.2 | 14.6 |
| Generously allowed (%) | – | 1.2 | 0.7 |
| Outliers (%) | 0.0 | 0.0 | 0.0 |
a
Numbers in parentheses indicate values for the outermost resolution shell.