Table 2.
X-ray diffraction data collection and refinement statistics for the DrBphP Y263F structures
| Parameters | CBD-Y263F | CBD-PHY-Y263F pre-illuminated | CBD-PHY-Y263F dark |
|---|---|---|---|
| Data collectiona | |||
| Space group | C121 | P 21 21 21 | P 21 21 21 |
| Cell dimensions | |||
| a, b, c (Å) | 94.24, 54.58, 70.56 | 85.7, 198.5, 223.6 | 84.1, 197.1, 214.1 |
| α, β, γ (degrees) | 90.00, 92.20, 90.00 | 90.0, 90.0, 90.0 | 90.0, 90.0, 90.0 |
| Resolution (Å) | 19.93–1.34 (1.38–1.34) | 19.98–3.30 (3.38–3.30) | 19.94–3.60 (3.69–3.60) |
| Rmerge | 0.059 (1.333) | 0.157 (1.469) | 0.072 (1.414) |
| CC½ | 0.998 (0.311) | 0.994 (0.312) | 0.999 (0.343) |
| I/σ(I) | 10.51 (0.89) | 7.68 (0.96) | 11.59 (0.90) |
| Completeness (%) | 99.8 (99.7) | 99.1 (99.9) | 96.6 (98.8) |
| Redundancy | 4.13 (3.94) | 4.09 (4.31) | 4.39 (4.52) |
| Wilson B factor | 18.2 | 99.8 | 164.2 |
| Refinement | |||
| Resolution (Å) | 19.93–1.34 (1.38–1.34) | 19.98–3.30 (3.38–3.30) | 19.94–3.60 (3.69–3.60) |
| No. of reflections | 76,244 (5617) | 54,898 (3899) | 38,682 (2783) |
| Rwork/Rfree | 0.143/0.182b (0.528/0.530) | 0.234/0.267 (0.389/0.391) | 0.248/0.287 (0.373/0.359) |
| Overall B factor | 26.0 | 115.0 | 197.0 |
| No. of atoms | |||
| Proteinc | 2336 | 14,790 | 14,443 |
| Ligandd | 63 | 172 | 172 |
| Water | 318 | 5 | 0 |
| Geometry | |||
| RMSD | |||
| Bond lengths (Å) | 0.014 | 0.007 | 0.007 |
| Bond angles (degrees) | 1.754 | 1.172 | 1.175 |
| Ramachandran (%) | |||
| Favored | 99 | 96 | 95 |
| Allowed | 1 | 4 | 5 |
| Outliers | 0 | 0 | 0 |
| PDB code | 5NFX | 5NM3 | 5NWN |
a Outer shell values are in parentheses.
b Test set for Rfree calculation constitutes 5% of total reflections that were randomly chosen.
c Number of protein molecules in an asymmetric unit: one (CBD-Y263F) and four (CBD–PHY-Y263F dark and pre-illuminated).
d This includes atoms from a biliverdin, three acetates and a (4S)-2-methyl-2,4-pentanediol (CBD-Y263F), or four biliverdins (pre-illuminated and dark CBD–PHY-Y263F).