Table 1. X-ray Diffraction Data Collection and Refinementa.
| Put2p | Put2p–NAD+ | HsP5CDH | |
|---|---|---|---|
| space group | P63 | P63 | P21 |
| unit cell dimensions | a = 109.0 Å, c = 181.2 Å | a = 108.0 Å, c = 181.0 Å | a = 92.0 Å, b = 121.3 Å, c = 93.4 Å, β = 104.2° |
| wavelength (Å) | 0.979 | 0.979 | 0.979 |
| resolution (Å) | 50.0–1.95 (2.02–1.95) | 93.6–2.17 (2.29–2.17) | 50.0–1.95 (2.02–1.95) |
| no. of observations | 579452 | 277102 | 489835 |
| no. of unique reflections | 88348 | 63148 | 139296 |
| Rmerge(I) | 0.061 (0.525) | 0.057 (0.583) | 0.049 (0.453) |
| mean I/σ | 32.1 (3.4) | 16.5 (2.3) | 24.2 (2.2) |
| completeness (%) | 99.9 (100.0) | 99.8 (98.9) | 96.5 (93.0) |
| multiplicity | 6.6 (6.5) | 4.4 (4.4) | 3.5 (3.3) |
| no. of protein residues | 971 | 961 | 2054 |
| no. of atoms | 7755 | 7578 | 15436 |
| no. of NAD+ atoms | 0 | 62 | 0 |
| no. of water molecules | 245 | 173 | 241 |
| no. of PEG atoms | 0 | 0 | 45 |
| no. of Mg2+ ions | 0 | 0 | 1 |
| Rcryst | 0.177 (0.211) | 0.173 (0.235) | 0.194 (0.228) |
| Rfreeb | 0.202 (0.240) | 0.212 (0.275) | 0.235 (0.301) |
| root-mean-square deviation for bond lengths (Å) | 0.007 | 0.008 | 0.007 |
| root-mean-square deviation for bond angles (deg) | 1.03 | 1.09 | 1.01 |
| Ramachandran plotc | |||
| favored (%) | 98.64 | 97.99 | 98.48 |
| outliers (no. of residues) | 0 | 0 | 0 |
| MolProbity score (percentile) | 100 | 99 | 100 |
| average B (Å2) | |||
| protein | 27.7 | 39.6 | 33.2 |
| NAD+ | – | 41.5 | – |
| water | 26.2 | 34.4 | 26.7 |
| PEG | – | – | 44.6 |
| Mg2+ | – | – | 40.5 |
| coordinate error (Å)d | 0.21 | 0.26 | 0.24 |
| PDB entry | 4OE6 | 4OE4 | 4OE5 |
a
Values for the outer resolution shell of data are given in parentheses.
b
A 5% test set. A common set was used for refinement of the Put2p structures.
c
The Ramachandran plots were generated with RAMPAGE via the PDB validation server.47
d
Maximum likelihood-based coordinate error estimate reported by PHENIX.