TABLE 1.
Crystallographic parameters and refinement statistics
| PDB code |
|||||
|---|---|---|---|---|---|
| 3A4G | 3A4H | 3A4Z | 3A50 | 3A51 | |
| Model | Vdh-WT | Vdh-WT | Vdh-K1 | Vdh-K1 | Vdh-K1 |
| Conformation | Open | Open | Closed | Closed | Closed |
| No. monomers in the AU | 1 | 1 | 5 | 5 | 5 |
| Substrates | Substrate-free | Substrate-free | Substrate-free | VD3 | 25(OH)VD3 |
| Data collection | |||||
| Beamline | PF-BL5A | PF-BL17A | AR-NE3A | AR-NE3A | AR-NW12A |
| Wavelength (Å) | 1.0000 | 1.0000 | 1.0000 | 1.0000 | 1.0000 |
| Space group | P31 | P212121 | P212121 | P212121 | P212121 |
| Unit cell parameters (Å, deg) | 61.7, 61.7, 98.8, 90, 90, 120 | 63.6, 65.8, 102.3, 90, 90, 90 | 77.4, 172.5, 189.9, 90, 90, 90 | 77.4, 172.3, 189.1, 90, 90, 90 | 77.2, 171.8, 189.1, 90, 90, 90 |
| Resolution range (Å)a | 50–1.75 (1.81–1.75) | 50–3.05 (3.16–3.05) | 50–2.20 (2.24–2.20) | 50–2.05 (2.09–2.05) | 50–2.00 (2.07–2.0) |
| Unique reflections | 42,012 | 8,366 | 129,009 | 158,815 | 170,383 |
| Redundancya | 5.3 (3.2) | 3.6 (3.8) | 7.3 (6.0) | 7.5 (6.3) | 7.4 (7.0) |
| Completeness (%)a | 99.3 (93.2) | 97.6 (97.9) | 100.0 (99.8) | 100.0 (99.8) | 100.0 (100.0) |
| I/σ (I)a | 21.9 (3.7) | 18.9 (6.0) | 26.0 (2.9) | 26.9 (2.9) | 32.5 (3.3) |
| Rmergea,b | 0.075 (0.316) | 0.090 (0.317) | 0.101 (0.500) | 0.107 (0.540) | 0.077 (0.594) |
| Wilson B-factor (Å2) | 23.2 | 45.0 | 27.9 | 23.3 | 29.5 |
| Refinement | |||||
| Rwork/Rfreec | 0.185/0.236 | 0.217/0.270 | 0.201/0.244 | 0.201/0.240 | 0.197/0.234 |
| R.m.s.deviation bond lengths (Å) | 0.015 | 0.006 | 0.015 | 0.013 | 0.014 |
| R.m.s.deviation bond angles (deg) | 1.53 | 0.96 | 1.56 | 1.50 | 1.55 |
| Total atoms | 3,451 | 3,138 | 16,621 | 16,977 | 17,293 |
| Average B-factors (Å2) | |||||
| Overall | 28.7 | 44.1 | 34.1 | 28.9 | 30.4 |
| Ligands | 35.3 (PEG) | 69.0 (VD3) | 41.3 (25(OH)VD3) | ||
| Ramachandran plot (%) | 89.6/10.4/0.0/0.0 | 89.5/10.5/0.0/0.0 | 91.1/8.9/0.0/0.0 | 90.6/9.4/0.0/0.0 | 90.6/9.4/0.0/0.0 |
a Data for the highest resolution shell are provided in parentheses.
b Rmerge = Σh Σi|Ih,i − 〈Ih〉|/ΣhΣi Ih,i, where 〈Ih〉 is the mean intensity of a set of equivalent reflections.
c Rwork = Σ|Fobs − Fcalc|/Σ Fobs for the 95% of the reflection data used in the refinement. Fobs and Fcalc are observed and calculated structure factor amplitudes, respectively. Rfree is the equivalent of Rwork, except that it was calculated for a randomly chosen 5% test set excluded from the refinement.