Table 3.
Crystallographic data collection and refinement statistics of EcOpgD and EcOpgG.
| Data set | Ligand-free EcOpgD (D378N mutant) | EcOpgD-Sop13 (D378N mutant) | EcOpgG-Sop16 (D361N mutant) |
|---|---|---|---|
| Data collection | |||
| Beamline | KEK BL-5A | KEK BL-5A | KEK BL-5A |
| Space group | C222 | P21 | C2221 |
| Unit cell parameters (Å) | a = 226.62 | a = 58.09 | a = 62.82 |
| b = 392.36 | b = 87.10 | b = 80.97 | |
| c = 324.48 | c = 110.85 | c = 213.23 | |
| β = 101.13° | |||
| Resolution (Å)a | 49.14–2.95 (3.00–2.95) | 47.74–2.06 (2.11–2.06) | 48.34–1.81 (1.85–1.81) |
| Total reflectionsa | 4,115,005 (209213) | 434,382 (21047) | 322,515 (19400) |
| Unique reflectionsa | 301,232 (14824) | 66,585 (4130) | 50,021 (2971) |
| Completeness (%)a | 100.0 (100.0) | 99.3 (92.6) | 99.9 (99.9) |
| Multiplicitya | 13.7 (14.1) | 6.5 (5.1) | 6.4 (6.5) |
| Mean I/σ(I)a | 13.0 (3.6) | 12.8 (2.1) | 17.2 (2.1) |
| Rmerge (%)a | 20.8 (87.8) | 11.6 (64.2) | 5.2 (76.2) |
| Rpim (%)a | 8.4 (35.1) | 7.4 (46.6) | 3.3 (48.9) |
| CC1/2a | (0.869) | (0.697) | (0.891) |
| Refinement | |||
| Resolution (Å) | 49.14–2.95 | 47.74–2.06 | 48.34–1.81 |
| No. of reflections | 301,231 | 63,310 | 49,959 |
| No. of atoms | 51,848 | 9013 | 4118 |
| No. of water molecules | 666 | 566 | 122 |
| Rwork/Rfree (%) | 19.4/23.2 | 17.5/22.4 | 21.3/25.4 |
| No. of asymmetric units | 12 | 2 | 1 |
| r.m.s.d. from ideal values | |||
| Bond lengths (Å) | 0.0087 | 0.0084 | 0.014 |
| Bond angles (°) | 1.6025 | 1.5974 | 1.719 |
| Average B-factors (Å2) | |||
| Protein (chain A/B/C/…) | 34.7/40.3/37.9/35.1/ | ||
| 35.3/37.9/34.6/40.5 | 24.1/24.4 | 45.1 | |
| /37.9/35.2/34.7/40.5 | |||
| Ligand | |||
| Sopns (chain A/B) | 18.8/22.1 | 34.6 | |
| Solvent | 32.0 | 25.8 | 34.4 |
| Ramachandran plot (%) | |||
| Favored | 94.6 | 97.0 | 96.0 |
| Allowed | 5.2 | 3.0 | 4.0 |
| Outlier | 0.2 | 0.0 | 0 |
| PDB entry | 8IOX | 8IP1 | 8IP2 |
aValues in parentheses represent the highest resolution shell.