Table 1.
X-ray data collection and refinement statistics
| Data collection | Wild-type PRF | C314S PRF-apo | C314S PRF-GSH |
|---|---|---|---|
| PDB code | 5VE3 | 5VE4 | 5VE5 |
| Space group | P212121 | P6522 | P6522 |
| Cell dimensions | |||
| a, b, c (Å) | 63.7, 108.3, 119.6 | 84.5, 84.5, 549.4 | 83.5, 83.5, 547.6 |
| α, β, γ (°) | 90, 90, 90 | 90, 90, 120 | 90, 90, 120 |
| X-ray source | APS 23ID-D | APS 23ID-B | APS 23ID-B |
| Wavelength (Å) | 1.033 | 1.033 | 1.033 |
| dmin (Å) | 1.79 (1.86–1.79)a | 2.65 (2.75–2.65) | 2.35 (2.43–2.35) |
| R-merge | 0.119 (1.47) | 0.126 (1.35) | 0.126 (1.56) |
| Inner-shell R-merge | 0.045 (5.3 Å)b | 0.047 (7.8 Å) | 0.050 (7.0 Å) |
| Average I/σ(I) | 14.6 (1.2) | 11.6 (1.7) | 11.0 (1.6) |
| Completeness (%) | 100 (96.0) | 100 (100) | 99.0 (99.0) |
| Multiplicity | 12.4 (9.0) | 8.6 (8.5) | 8.7 (9.2) |
| Total observations | 966,980 (67,309) | 303,925 (28,966) | 422,379 (43,869) |
| CC1/2 | 0.999 (0.537) | 0.997 (0.898) | 0.998 (0.904) |
| CC* | 1.0 (0.836) | 0.999 (0.973) | 0.999 (0.975) |
| Refinement | |||
| Data range (Å) | 41.26–1.79 | 43.94–2.65 | 41.75–2.35 |
| Reflections used in refinement | 77,982 (7448) | 35,305 (3392) | 48,680 (4773) |
| Rwork/Rfree (%) | 16.1/19.6 | 23.2/26.7 | 19.7/25.2 |
| No. of non-hydrogen atoms | 6051 | 8265 | 8471 |
| Protein | 5538 | 8153 | 8154 |
| Ligands | 2 | 24 | 74 |
| Water | 511 | 88 | 189 |
| Amino acid residues | 698 | 1047 | 1048 |
| Deviation from ideality | |||
| Bond lengths (Å) | 0.013 | 0.003 | 0.007 |
| Bond angles (°) | 1.20 | 0.70 | 0.97 |
| Average B-factor | 38.1 | 81.9 | 76.6 |
| Macromolecules | 37.6 | 82.4 | 77.0 |
| Ligands | 29.6 | 59.0 | 83.1 |
| Solvent | 44.1 | 45.6 | 58.4 |
| Ramachandran plot | |||
| Favored (%) | 98.0 | 96.0 | 97.5 |
| Allowed (%) | 2.0 | 4.0 | 2.3 |
| Outliers (%) | 0 | 0 | 0.2 |
a Values in parentheses pertain to the outermost shell of data.
b dmin inner shell is shown.