Table 2.
Data collection and refinement statistics
| Data set |
||||
|---|---|---|---|---|
| Ligand-free | Sop3 complex | Sop4 complex | Sop5 complex | |
| Data collection | ||||
| Space group | P32 | P21 | P1 | P21 |
| Cell dimensions (Å) | a = b = 74.9, c = 120.8 | a = 36.1, b = 125.6, c = 91.8 | a = 36.0, b = 63.3, c = 87.5 | a = 36.2, b = 126.0, c = 91.0 |
| Angles (°) | β = 101.6 | α = 90.0, β = 82.2, γ = 86.1 | β = 100.5 | |
| Resolution (Å)a | 50.0–2.20 (2.24–2.20) | 50.0–2.10 (2.14–2.10) | 50.0–1.60 (1.63–1.60) | 50.0–1.90 (1.93–1.90) |
| Total reflections | 208,593 | 160,585 | 337,940 | 232,606 |
| Unique reflectionsa | 38,141 (1,912) | 44,909 (2,234) | 98,051 (4,453) | 61,562 (2,964) |
| Completeness (%)a | 98.8 (100.0) | 96.5 (96.5) | 96.0 (87.0) | 97.5 (95.6) |
| Redundancya | 5.5 (5.7) | 3.6 (3.5) | 3.4 (3.3) | 3.8 (3.7) |
| Mean I/σIa | 21.0 (2.7) | 12.4 (1.7) | 20.7 (1.5) | 16.2 (2.1) |
| Rmerge (%)a | 9.7 (57.1) | 11.6 (63.9) | 6.8 (73.7) | 9.9 (54.5) |
| Rpim (%)a | 4.7 (26.3) | 7.1 (38.9) | 4.3 (47.4) | 5.9 (32.3) |
| CC1/2a | (0.906) | (0.697) | (0.617) | (0.824) |
| Refinement | ||||
| Resolution (Å) | 19.2–2.20 | 45.0–2.10 | 43.3–1.60 | 44.8–1.90 |
| No. of reflections | 36,488 | 42,614 | 92,359 | 58,354 |
| Rwork/Rfree (%) | 19.0/24.7 | 16.9/20.7 | 15.8/18.8 | 16.6/20.3 |
| No. of atoms | 6,335 | 6,538 | 6,899 | 6,765 |
| No. of water molecules | 205 | 286 | 632 | 455 |
| r.m.s.d. from ideal values | ||||
| Bond lengths (Å) | 0.016 | 0.019 | 0.020 | 0.018 |
| Bond angles (°) | 1.667 | 1.851 | 1.855 | 1.864 |
| Average B-factors (Å2) | ||||
| Protein (chain A/B) | 50.6/49.3 | 49.1/67.2 | 36.3/60.7 | 29.1/36.7 |
| Ligand | 24.4 | 20.4 | 27.0 | |
| Water | 46.8 | 33.2 | 35.7 | 33.3 |
| Zinc ion | 73.0 | |||
| Di(hydroxyethyl)ether | 60.0 | |||
| MPD | 48.5 | 41.4 | 44.7 | |
| Magnesium ion | 33.4 | 31.8 | 29.4 | |
| Ramachandran plot (%) | ||||
| Favored | 97.8 | 98.7 | 99.2 | 98.3 |
| Allowed | 2.2 | 1.3 | 0.8 | 1.7 |
| Outlier | 0 | 0 | 0 | 0 |
| PDB code | 5YSB | 5YSD | 5YSE | 5YSF |
a Values in parentheses denote the highest resolution shell.