TABLE 2.
Crystallographic data collection and refinement statistics for ygiF
Highest resolution shell is shown in parenthesis.
| ygiF (NaI soak) | ygiF/PPPi/Mg2+ | ygiF/PPPi/Mn2+ | ygiF/PPPi/Mn2+ (Mn-K edge) | |
|---|---|---|---|---|
| PDB ID | 5a60 | 5a61 | ||
| Data collection | ||||
| Beam line | SLS PXII | SLS PXII | SLS PXII | SLS PXII |
| Wavelength (Å) | 1.9 | 1.0 | 1.0 | 1.7 |
| Space group | P65 | P65 | P65 | P65 |
| Cell dimensions | ||||
| a = b, c (Å) | 91.11, 125.56 | 89.92, 125.58 | 89.68, 125.33 | 89.95, 125.31 |
| α, β, γ (°) | 90, 90, 120 | 90, 90, 120 | 90, 90, 120 | 90, 90, 120 |
| Resolution (Å) | 49.127-2.70 | 48.88-1.82 | 48.77-1.50 | 48.74-1.86 |
| (2.87-2.70) | (1.93-1.82) | (1.59-1.50) | (1.97-1.86) | |
| Rsym | 0.077 (0.186) | 0.068 (0.944) | 0.036 (1.20) | 0.037 (0.313) |
| I/σI | 31.08 (11.28) | 14.91 (2.18) | 23.90 (1.93) | 26.80 (3.91) |
| Completeness (%) | 95.8 (90.2) | 98.8 (96.9) | 99.7 (98.3) | 97.9 (90.2) |
| Redundancy | 19.63 (18.47) | 9.70 (9.06) | 15.48 (14.18) | 8.30 (3.55) |
| Refinement | ||||
| Resolution (Å) | 48.88-1.82 | 48.77–1.50 | ||
| No. reflections | 47,520 | 86,573 | ||
| Rwork/ Rfree | 0.150/0.189 | 0.151/0.171 | ||
| No. atoms | ||||
| Protein | 3398 | 3395 | ||
| Pi/PPi/PPPi | 13 | 13 | ||
| Mg2+/Mn2+ | 2 | 2 | ||
| Water | 289 | 295 | ||
| B-factors | ||||
| Protein | 55.83 | 52.41 | ||
| Pi/PPi/PPPi | 46.83 | 42.84 | ||
| Mg2+/Mn2+ | 46.65 | 42.53 | ||
| Water | 58.34 | 58.82 | ||
| r.m.s.d. | ||||
| Bond lengths (Å) | 0.007 | 0.006 | ||
| Bond angles (°) | 1.149 | 1.186 | ||
| Ramachandran plot (%) | ||||
| Favored | 99.1 | 99.3 | ||
| Outliers | 0 | 0 | ||