Table 1.
X-ray Diffraction Data Collection and Refinementa
| AfUGMo-NADPH | AfUGMo-NADH | AfUGMr | |
|---|---|---|---|
| Data collection
| |||
| Soaking ligand | NADPH | NADH | NADPH |
| Soaking time (min.) | 1 | 1 | 30 |
| Flavin redox state | oxidized | oxidized | reduced |
| Space group | P6522 | P6522 | P6522 |
| Unit cell parameters (Å) | a =218.3, c = 319.2 | a =218.3, c = 318.1 | a = 217.4, c = 319.9 |
| Wavelength (Å) | 0.979 | 0.979 | 0.979 |
| Resolution (Å) | 163-2.75 (2.90-2.75) | 162-2.75 (2.90-2.75) | 50-2.20 (2.32-2.20) |
| Observations | 851567 | 982507 | 984169 |
| Unique reflections | 116001 | 115207 | 222394 |
| Rmerge(I)b | 0.137 (0.885) | 0.158 (1.216) | 0.093 (0.673) |
| Rmeas(I)b | 0.147 (0.967) | 0.168 (1.297) | 0.106 (0.778) |
| Rpim(I)b | 0.054 (0.382) | 0.054 (0.429) | 0.049 (0.383) |
| Mean I/σ | 11.6 (2.2) | 10.9 (2.1) | 9.8 (2.0) |
| Completeness (%) | 99.9 (99.9) | 99.6 (99.9) | 99.7 (99.8) |
| Multiplicity | 7.3 (6.1) | 8.5 (7.9) | 4.4 (4.0) |
|
| |||
| Refinement
| |||
| Resolution (Å) | 163-2.75 (2.78-2.75) | 162-2.75 (2.78-2.75) | 48-2.20 (2.28-2.20) |
| No. of protein residues | 1987 | 1989 | 2017 |
| No. of protein atoms | 15008 | 15164 | 15526 |
| No. of FAD atoms | 212 | 212 | 212 |
| No. of NAD(P)H molecules/atoms | 4/158 | 2/88 | 0/0 |
| NAD(P)H occupancyc | 0.7–0.9 | 0.9 | - |
| No. of water molecules | 16 | 26 | 435 |
| Rcryst | 0.210 (0.299) | 0.212 (0.404) | 0.201 (0.293) |
| Rfreed | 0.246 (0.318) | 0.245 (0.391) | 0.227 (0.343) |
| rmsd bond lengths (Å)e | 0.008 | 0.008 | 0.007 |
| rmsd bond angles (°)e | 1.17 | 1.19 | 1.05 |
| Ramachandran plotf | |||
| Favored (no. residues) | 1908 | 1919 | 1978 |
| Allowed (no. residues) | 59 | 50 | 31 |
| Outliers (no. residues) | 0 | 0 | 0 |
| Average B-factor (Å2) | |||
| Protein | 53 | 51 | 41 |
| FAD | 52 | 53 | 37 |
| NAD(P)Hc | 48–72 | 50–52 | - |
| Water | 36 | 41 | 37 |
| Coordinate error (Å)g | 0.41 | 0.51 | 0.36 |
| PDB code | 4gdc | 4gdd | 4gde |
a
Values for the outer resolution shell of data are given in parenthesis.
b
Definitions of Rmerge, Rmeas, and Rpim can be found in Weiss.23
c
Range reflects the ligands bound to different chains of the tetramer.
d
A common set of test reflections (5 %) was used for refinement of all structures.
e
Compared to the parameters of Engh and Huber.24
f
The Ramachandran plot was generated with RAMPAGE.25
g
Maximum likelihood-based coordinate error estimate from PHENIX.