Table 4. X-ray Diffraction Data Collection and Refinementa.
D779W | D779Y | D778Y | |
---|---|---|---|
space group | C2 | C2 | C2 |
unit cell parameters | a = 166.9 Å | a = 167.1 Å | a = 166.1 Å |
b = 195.3 Å | b = 196.0 Å | b = 195.1 Å | |
c = 108.8 Å | c = 108.7 Å | c = 108.4 Å | |
β = 121.6° | β = 121.4° | β = 121.5° | |
wavelength (Å) | 1.000 | 1.000 | 1.000 |
diffraction resolution (Å) | 32.0–2.20 (2.32–2.20) | 32.0–2.30 (2.42–2.30) | 46.9–2.30 (2.42–2.30) |
no. of observations | 549668 | 490658 | 485882 |
no. of unique reflections | 149604 | 130815 | 130019 |
Rmerge(I) | 0.106 (0.464) | 0.103 (0.515) | 0.095 (0.524) |
Rmeas(I) | 0.124 (0.556) | 0.120 (0.602) | 0.112 (0.612) |
Rpim(I) | 0.063 (0.302) | 0.061 (0.310) | 0.058 (0.314) |
mean I/σ | 6.8 (2.1) | 8.1 (2.2) | 10.0 (2.5) |
completeness (%) | 99.9 (99.3) | 99.3 (98.8) | 99.9 (100) |
multiplicity | 3.7 (3.3) | 3.8 (3.6) | 3.7 (3.8) |
no. of protein chains | 2 | 2 | 2 |
no. of protein residues | 1943 | 1943 | 1941 |
no. of protein atoms | 14390 | 14386 | 14490 |
no. of FAD atoms | 106 | 106 | 106 |
no. of water molecules | 531 | 296 | 419 |
no. of sulfate ions | 6 | 6 | 8 |
no. of glycerol molecules | 4 | 3 | 4 |
Rcryst | 0.208 | 0.216 | 0.195 |
Rfreeb | 0.241 | 0.251 | 0.235 |
root-mean-square deviation for bond lengths (Å) | 0.008 | 0.008 | 0.009 |
root-mean-square deviation for bond angles (deg) | 1.102 | 1.107 | 1.106 |
Ramachandran plotc | |||
favored (%) | 98.8 | 98.1 | 98.1 |
outliers (no. of residues) | 2 | 2 | 0 |
average B factors (Å2) | |||
protein | 31.5 | 38.9 | 34.5 |
FAD | 20.0 | 29.3 | 25.2 |
water | 28.5 | 31.8 | 30.4 |
sulfate | 61.4 | 67.6 | 74.3 |
glycerol | 36.5 | 47.3 | 45.3 |
coordinate error (Å)d | 0.27 | 0.31 | 0.28 |
PDB entry | 4Q71 | 4Q72 | 4Q73 |
Values for the outer resolution shell of data are given in parentheses.
A 5% random test set. A common set was used for refinement of all structures.
The Ramachandran plot was generated with RAMPAGE.46
Maximum likelihood-based coordinate error estimate reported by PHENIX.