Table 1.
Data Collection and Refinement Statistics for Y540S Structuresa
| Ligand | THFA | hydroxyproline | proline |
|---|---|---|---|
| Space group | I222 | I222 | I222 |
| Unit cell lengths (Å) | a = 72.6 | a = 73.4 | a = 73.1 |
| b = 140.1 | b = 142.6 | b = 140.9 | |
| c = 146.7 | c = 145.7 | c = 145.3 | |
| Wavelength (Å) | 0.97922 | 0.97949 | 1.00000 |
| Diffraction resolution (Å) | 46.1 – 1.85 (1.92 – 1.85) | 50.0 – 1.75 (1.78 – 1.75) | 27.7 – 1.90 (2.00 – 1.90) |
| No. of observations | 386345 | 453150 | 249908 |
| No. of unique reflections | 63740 | 76563 | 58713 |
| Redundancy | 6.1 (5.6) | 5.9 (5.5) | 4.3 (3.3) |
| Completeness (%) | 99.5 (95.7) | 99.3 (98.5) | 99.2 (95.1) |
| Rmerge(I) | 0.059 (0.481) | 0.047 (0.418) | 0.079 (0.417) |
| Average I/⌠ | 26.7 (2.1) | 37.8 (2.5) | 13.1 (3.3) |
| Wilson B-factor (Å2) | 24.2 | 27.0 | 21.4 |
| No. of protein chains | 1 | 1 | 1 |
| No. of atoms | 3937 | 3930 | 3808 |
| No. of protein residues | 468 | 468 | 471 |
| No. of water molecules | 266 | 252 | 143 |
| Rcryst | 0.198 (0.231) | 0.201 (0.231) | 0.212 (0.327) |
| Rfreeb | 0.227 (0.283) | 0.228 (0.260) | 0.242 (0.326) |
| RMSDc | |||
| Bond lengths (Å) | 0.006 | 0.006 | 0.008 |
| Bond angles (deg.) | 0.96 | 1.06 | 1.11 |
| Ramachandran plotd | |||
| Favored (%) | 98.5 | 98.9 | 98.9 |
| Allowed (%) | 1.5 | 1.1 | 1.1 |
| Outliers (%) | 0.0 | 0.0 | 0.0 |
| Average B-factors (Å2) | |||
| Protein | 33.3 | 39.2 | 39.8 |
| FAD | 19.0 | 24.0 | 22.4 |
| ligand | 23.2 | 37.9 | 26.5 |
| water | 34.3 | 38.4 | 31.8 |
| Coordinate error (Å)e | 0.21 | 0.21 | 0.26 |
| PDB accession code | 3E2R | 3E2Q | 3E2S |
a
Values for the outer resolution shell of data are given in parenthesis.
b
5% test set. A common set of test reflections was used for refinement of all structures.
c
Compared to the Engh and Huber parameters (36).
d
The Ramachandran plot was generated with RAMPAGE (37).
e
Maximum likelihood-based coordinate error reported by PHENIX.