Table 1. X-ray Data and Refinement Statistics for Horse Alcohol Dehydrogenases.
| enzyme complex, zinc ligand | apoenzyme, H2O | ADPR, H2O | 2,2′-bipyridine | 1,10-phenanthroline | NADH, H2O | NADH, MHF | NADH, BNF |
|---|---|---|---|---|---|---|---|
| PDB entry | 1YE3 | 5VKR | 5VJG | 5VJ5 | 4XD2 | 5VN1 | 5VL0 |
| space group, no. of subunits per asymmetric unita | C2221, 1 | C2221, 1 | C2221, 1 | P212121, 2 | P1, 2 | P21, 4 | P21, 4 |
| cell dimensions (Å) | 55.8, 74.3, 181.3 | 55.4, 74.3, 181.0 | 55.5, 73.7, 181.1 | 55.3, 73.4, 180.8 | 44.2, 50.9, 92.7 | 50.2, 180.8, 86.8 | 50.2, 180.3, 86.9 |
| cell angles (deg) | 90, 90, 90 | 90, 90, 90 | 90, 90, 90 | 90, 90, 90 | 92.0, 103.0, 109.6 | 90, 106.1, 90 | 90, 106.2, 90 |
| mosaicity | 0.92 | 0.74 | 1.2 | 1.1 | 1.1 | 0.94 | |
| resolution range (Å) (shell) | 20.1–1.59 (1.63) | 19.93–1.80 (1.86) | 19.9–1.90 (1.97) | 19.84–1.90 (1.97) | 19.8–1.1 (1.13) | 20.0–1.25 (1.30) | 20.0–1.2 (1.24) |
| no. of reflections (total, unique)b | 205694, 36732 | 245973, 30816 | 198230, 27148 | 300828, 55508 | 687793, 257968 | 611039, 325043 | 2260931, 361271 |
| redundancy (shell) | 5.61 (5.43) | 7.64 (5.68) | 6.99 (5.04) | 5.30 (3.38) | 2.8 (1.89) | 1.79 (1.59) | 6.19 (4.34) |
| completeness (%) (outer shell) | 71.9 (54.0) | 91.7 (85.6) | 95.3 (87.4) | 96.1 (93.3) | 86.8 (71.1) | 80.0 (72.7) | 79.4 (57.4) |
| Rpim (%) (outer shell)c | 3.8 (9.9) | 4.6 (23.2) | 4.8 (17.0) | 3.8 (24.9) | 2.9 (39.6) | 8.9 (25.5) | 3.8 (27.7) |
| mean ⟨I⟩/σ⟨I⟩ (outer shell) | 12.9 (4.9) | 9.0 (2.1) | 9.8 (3.5) | 8.8 (2.9) | 9.1 (2.3) | 6.6 (2.2) | 8.3 (1.7) |
| Rvalue, Rfree (%) (test %, no.)d | 20.1, 25.6 (3.1, 1143) | 19.2, 24.8 (4.1, 1328) | 20.9, 28.3 (4.1, 1174) | 24.8, 29.4 (2.1, 1169) | 17.7, 19.8 (0.5, 1292) | 15.2, 18.7 (0.5, 1650) | 15.9, 19.9 (1.0, 3775) |
| RMSD for bond distances (Å)e | 0.014 | 0.019 | 0.016 | 0.016 | 0.014 | 0.017 | 0.019 |
| RMSD for bond angles (deg)e | 1.53 | 2.07 | 1.80 | 1..81 | 1.75 | 1.89 | 2.06 |
| estimated error in coordinates (Å) | 0.069 | 0.125 | 0.153 | 0.195 | 0.032 | 0.028 | 0.036 |
| mean B value (Wilson, Refmac) (Å2) | 25.4, 35.4 | 43.6, 50.6 | 29.2, 41.4 | 22.5, 35.7 | 8.8, 19.1 | 19.0, 25.0 | 13.0, 20.3 |
| total no. of non-H atoms (mean B value) | 2995 | 2868 | 2895 | 5828 | 6719 | 12774 | 12940 |
| protein | 2748 (32.0) | 2785 (51.5) | 2799 (41.0) | 5568 (36.8) | 5764 (17.7) | 11195 (24.8) | 11343 (19.8) |
| heteroatoms, zinc, ligands | 10 (54.0) | 38 (59.5) | 14 (46.5) | 32 (27.7) | 126 (21.2) | 250 (26.0) | 240 (19.6) |
| waters | 200 (39.6) | 45 (51.4) | 96 (40.5) | 228 (38.4) | 829 (36.8) | 1329 (37.0) | 1357 (32.5) |
| Ramachandran (%) (favored, outlier) | 97.6, 0 | 96.0, 0 | 95.2, 0.27 | 96.0, 0.54 | 97.2, 0 | 97.2, 0 | 97.1, 0 |
| MolProbity (clash, score, rank %) | 3.71 (97th), 1.33 (95th) | 2.99 (99th), 1.72 (83rd) | 1.77 (100th), 1.49 (96th) | 1.94 (100th), 1.75 (85th) | 1.5 (97th), 1.03 (98th) | 1.34 (98th), 1.05 (99th) | 1.36 (98th), 1.01 (99th) |
a
The biological molecule is a dimer of identical protein subunits.
b
Data cutoff, σF > 0.
c
Rpim = Rmerge/(n – 1)1/2, where n is data redundancy.
d
Rvalue = (∑|Fo – kFc|)/∑|Fo|, where k is a scale factor. Rfree was calculated with the indicated percentage of reflections not used in the refinement.104
e
Deviations from ideal geometry.