Table 1 Data collection and refinement statistics of the V1-ATPase.
From: Crystal structures of the ATP-binding and ADP-release dwells of the V1 rotary motor
Denoted as | 2 ATP V 1 | 2 ADP V 1 | 3 ADP V 1 | 0 Pi V 1 :20 μM | 0 Pi V 1 :200 μM | 1 Pi V 1 |
|---|---|---|---|---|---|---|
Crystallization condition | ||||||
Soaking with | 2 mM AMP-PNP 3 mM MgCl2 | 20 μM ADP 3 mM MgSO4 | 2 mM ADP 3 mM MgSO4 | 20 μM Pi 3 mM MgCl2 | 200 μM Pi 3 mM MgCl2 | 2 mM Pi 3 mM MgCl2 |
Soaking time | 6.5 h | 4.5 h | 4.5 h | 5.5 h | 5.0 h | 5.0 h |
Data collection | ||||||
Beamline | PF BL1A | PF BL1A | PF BL1A | PF BL17A | PF BL1A | PF BL1A |
Wavelength (Å) | 1.1000 | 1.1000 | 1.1000 | 0.9800 | 1.1000 | 1.1000 |
Space group | P212121 | P212121 | P212121 | P212121 | P212121 | P212121 |
Cell dimensions | ||||||
a, b, c (Å) | 128.3, 128.4, 226.9 | 127.4, 129.6, 237.2 | 121.7, 126.5, 225.3 | 128.5, 128.5, 226.5 | 127.9, 128.4, 226.7 | 128.2, 128.4, 228.0 |
α,β,γ (°) | 90.0, 90.0, 90.0 | 90.0, 90.0, 90.0 | 90.0, 90.0, 90.0 | 90.0, 90.0, 90.0 | 90.0, 90.0, 90.0 | 90.0, 90.0, 90.0 |
Resolution (Å) | 50–2.73 (2.89–2.73)* | 50–3.25 (3.45–3.25) | 50–3.02 (3.21-3.02) | 50–3.04 (3.23-3.04) | 50–2.84 (3.01-2.84) | 49.04–2.89 (2.99-2.89) |
Rmerge | 0.170 (0.916) | 0.199 (1.064) | 0.221 (1.064) | 0.251 (0.873) | 0.222 (0.961) | 0.157 (0.824) |
I/σI | 10.14 (1.87) | 10.33 (1.88) | 10.08 (1.92) | 8.79 (2.08) | 9.34 (1.99) | 12.5 (2.2) |
Completeness (%) | 98.9 (94.4) | 99.4 (97.2) | 99.2 (95.4) | 99.7 (99.2) | 99.7 (98.7) | 99.9 (100) |
Redundancy | 6.5 (6.3) | 6.7 (6.6) | 6.6 (6.5) | 6.3 (6.5) | 6.7 (6.8) | 6.6 (5.3) |
Refinement | ||||||
Resolution (Å) | 50–2.73 | 50–3.25 | 50–3.02 | 48.93–3.04 | 50–2.84 | 49.04–2.89 |
No. of reflections | 99,064 | 62,128 | 67,952 | 72,486 | 88,898 | 84,446 |
Rwork/ Rfree (%) | 20.5/23.2 | 20.9/24.5 | 21.4/25.3 | 23.0/27.3 | 18.5/20.1 | 20.7/25.1 |
No. of atoms | ||||||
Protein | 26,653 | 25,976 | 26,554 | 26,389 | 26,414 | 26,309 |
Ligand/ion | 137 | 68 | 173 | 44 | 80 | 43 |
Water | 299 | 33 | 72 | 29 | 268 | 64 |
B-factors | ||||||
Protein | 55.37 | 83.02 | 55.82 | 49.78 | 44.90 | 64.84 |
Ligand/ion | 47.81 | 57.03 | 57.91 | 56.10 | 50.85 | 70.55 |
Water | 38.22 | 52.84 | 39.93 | 17.61 | 29.66 | 46.61 |
r.m.s. deviations | ||||||
Bond lengths (Å) | 0.004 | 0.003 | 0.003 | 0.002 | 0.002 | 0.003 |
Bond angles (°) | 0.872 | 0.673 | 0.660 | 0.548 | 0.678 | 0.757 |
PDB ID | – | 5KNB | 5KNC | – | – | 5KND |
