Table 3.
Data collection and refinement statistics
| PvNVPd P21_Peak | PvNVPd P21 (5YKZ) | PvNVPd P212121 (5YL0) | MrNVPd P3221_Peak | MrNVPd P3221 (5YKU) | MrNVPd C2221 (5YKV) | MrNVPd P4332 (5YKX) | T = 1 ΔN-ARM-PvNVSd SVPs (5YL1) | |
|---|---|---|---|---|---|---|---|---|
| Data collection | ||||||||
| Beamlinea | TLS 15A1 | TLS 15A1 | BL44XU | TLS 13C1 | TLS 13C1 | BL44XU | BL44XU | TPS 05A |
| Wavelength (Å) | 0.979 | 1.000 | 0.900 | 0.976 | 0.976 | 0.900 | 0.900 | 1.000 |
| Temperature (K) | 110 | 110 | 100 | 110 | 110 | 100 | 100 | 110 |
| Space group | P21 | P21 | P212121 | P3221 | P3221 | C2221 | P4332 | P212121 |
| Cell dimensions | ||||||||
| a, b, c (Å) | 42.72, 53.14, 46.38 | 42.60, 53.19, 46.07 | 43.84, 69.74, 146.61 | 72.87, 72.87, 47.04 | 72.87, 72.87, 47.04 | 125.77, 147.28, 175.92 | 134.18, 134.18, 134.18 | 196.98, 200.32, 419.29 |
| α, β, γ (°) | 90.00, 109.52, 90.00 | 90.00, 109.38, 90.00 | 90.00, 90.00, 90.00 | 90.00, 90.00, 120.00 | 90.00, 90.00, 120.00 | 90.00, 90.00, 90.00 | 90.00, 90.00, 90.00 | 90.00, 90.00, 90.00 |
| Resolution (Å)b | 30–1.28 (1.33–1.28) |
30–1.17 (1.21–1.17) |
30–1.22 (1.26–1.22) |
30–1.39 (1.44–1.39) |
30–1.39 (1.44–1.39) |
30–2.30 (2.38–2.30) |
30–2.00 (2.07–2.00) |
30–3.12 (3.23–3.12) |
| Rsym (%)b | 3.6 (16.7) | 7.7 (41.0) | 11.2 (43.8) | 7.0 (33.7) | 7.0 (33.7) | 14.2 (63.0) | 11.2 (83.0) | 21.8 (86.0) |
| I/σIb | 3.6 (16.7) | 7.7 (41.0) | 11.2 (43.8) | 7.0 (33.7) | 7.0 (33.7) | 14.2 (63.0) | 20.3 (19.0) | 5.0 (5.0) |
| Completeness (%)b | 98.2 (96.6) | 99.1 (92.4) | 86.9 (86.9) | 99.2 (98.4) | 99.2 (98.4) | 99.3 (97.6) | 99.9 (99.8) | 99.7 (99.8) |
| Redundancyb | 8.3 (8.3) | 4.6 (4.3) | 4.5 (4.8) | 9.6 (9.6) | 9.6 (9.6) | 5.3 (4.9) | 20.3 (19.0) | 5.0 (5.0) |
| Refinement | ||||||||
| Resolution (Å) | 30–1.17 | 30–1.22 | 30–1.39 | 30–2.30 | 30–2.00 | 30–3.12 | ||
| No. of reflections | 58,534 | 110,940 | 27,637 | 66,484 | 27,072 | 274,292 | ||
| Rwork/Rfree | 15.2/16.9 | 17.5/22.0 | 14.2/15.1 | 16.0/19.8 | 15.6/19.5 | 21.9/22.1 | ||
| No. of atoms | ||||||||
| Protein | 1681 | 3321 | 958 | 7748 | 1880 | 1454 | ||
| Ligand | – | – | – | – | 15 | – | ||
| SO4 | – | – | – | – | 5 | – | ||
| Metal | – | – | 3(Zn) | – | 3(Cd) | 2 (Ca) | ||
| Water | 414 | 1477 | 275 | 736 | 308 | – | ||
| B-factors | ||||||||
| Protein | 16.43 | 14.35 | 12.25 | 29.90 | 27.26 | 64.58 | ||
| Ligand | – | – | – | – | 80.26 | – | ||
| SO4 | – | – | – | – | 48.65 | – | ||
| Metal | – | – | 10.97 | – | 25.54 | 73.41 | ||
| Water | 30.03 | 36.67 | 27.90 | 38.87 | 52.11 | – | ||
| R.m.s. deviations | ||||||||
| Bond lengths (Å) | 0.027 | 0.027 | 0.028 | 0.011 | 0.022 | 0.011 | ||
| Bond angles (°) | 2.117 | 2.137 | 2.368 | 1.447 | 2.221 | 1.696 | ||
aOne crystal for each structure was used
bValues in parentheses are for highest-resolution shell