Table 1.
Data collection, phasing and refinement statistics for E. coli Ftp and S. oneidensis NqrC structures
| Crystal | E. coli Ftp | E. coli Ftp E169K | E. coli Ftp Y60N + ADP | S.oneidensis NqrC, native | S. oneidensis NqrC, Se1 peak |
|---|---|---|---|---|---|
| Data collection | |||||
| Wavelength (Å) | 0.97918 | 0.97718 | 0.97918 | 0.97918 | 0.97934 |
| Space group | P1 | P1 | P212121 | P21 | P212121 |
| Cell constants a, b, c, α, β, γ | 56.20, 70.65, 85.96, 75.70, 72.45, 69.28 | 57.22, 70.65, 86.28, 75.72, 71.91, 69.72 | 54.58, 56.98, 224.77, 90.0, 90.0, 90.0 | 70.91, 93.48, 71.14, 90.0, 100.24, 90.0 | 43.78, 132.05, 251.40, 90.0, 90.0, 90.0 |
| Resolution range (Å) | 31.5–1.88 (1.91–1.88) | 33.8–1.75 (1.78–1.75) | 29.6–1.85 (1.88–1.85) | 33.7–1.76 (1.79–1.76) | 37.2–2.82 (2.87–2.82) |
| Unique reflections | 91,038 (4488) | 116,958 (5748) | 57,017 (1856) | 89,381 (4319) | 36,559 (1546) |
| Multiplicity | 2.1 (2.1) | 3.7 (3.6) | 4.1 (3.4) | 4.1 (3.4) | 7.7 (5.4) |
| Data completeness (%) | 96.9 (94.5) | 97.3 (96.0) | 93.6 (60.7) | 99.0 (96.3) | 99.2 (86.1) |
| R merge (%)2 | 6.4 (58.1) | 8.7 (85.5) | 3.9 (60.6) | 6.5 (38.4) | 7.4 (30.9) |
| I/σ(I) | 13.7 (1.8) | 20.7 (1.8) | 29.6 (1.34) | 15.9 (2.56) | 24.8 (4.64) |
| Wilson B‐value (Å2) | 20.5 | 18.6 | 18.8 | 59.2 | 47.1 |
| Phase determination | |||||
| Anomalous scatterers | Selenium, 36 out of 36 possible sites | ||||
| Figure of merit (42.7–2.82 Å) | 0.40 | ||||
| Crystal | E. coli ApbE | E. coli ApbE E169K | E. coli Y60N + ADP | S. oneidensis NqrC, native |
|---|---|---|---|---|
| Refinement statistics | ||||
| Resolution range (Å) | 31.5–1.88 (1.90–1.88) | 33.8–1.75 (1.77–1.75) | 28.3–1.90 (1.94–1.90) | 37.1–1.76 (1.80–1.76) |
| No. of reflections R work/R free | 90,849/4543 (2561/148) | 116,560/5873 (3192/188) | 49,844/2495 (1110/56) | 88,913/2032 (5722/132) |
| Data completeness (%) | 96.4 (85.0) | 96.6 (84.0) | 88.4 (38.0) | 98.3 (89.0) |
| Twin law/twin fraction | NA | NA | NA | l,‐k,h/0.380 |
| Atoms (non‐H protein/solvent/metals/nucleotide or cofactor) | 9549/832/6/0 | 9458/695/7/0 | 4512/424/4/54 | 6955/651/1/120 |
| R work (%) | 16.4 (29.5) | 17.2 (24.4) | 18.0 (22.6) | 16.6 (23.5) |
| R free (%) | 20.0 (39.7) | 19.8 (30.0) | 21.4 (24.9) | 20.2 (24.8) |
| R.m.s.d. bond length (Å) | 0.007 | 0.006 | 0.017 | 0.004 |
| R.m.s.d. bond angle (°) | 0.96 | 0.87 | 0.99 | 0.65 |
| Mean B‐value (Å2) (protein/solvent/metals/nucleotide or cofactor) | 30.6/33.3/26.4/NA | 30.5/31.5/29.0/NA | 29.7/36.3/31.1/37.2 | 21.2/22.5/16.5/25.2 |
| Ramachandran plot (%) (favored/additional/disallowed)2 | 98.2/1.6/0.2 | 98.0/1.9/0.1 | 97.4/2.4/0.2 | 97.5/2.5/0.0 |
| Missing residues | A: 1–11, 216–221, 245–246, 329–341B: 1–12, 216–223, 330–341C: 1–12, 116–118, 217–221, 330–341D: 1–12, 216–222, 243–247, 330–341 | A: 1–11, 120–121, 214–222, 245–246, 329–341B: 1–12, 216–223, 330–341C: 1–12, 116–119, 217–222, 330–341D: 1–12, 216–223, 242–247, 330–341 | A: 1–12, 115–121, 213–223, 242–250, 330–341B: 1–12, 116–120, 215–223, 242–251, 330–341 | A: −27 to −1, 255 to 264B: −27 to −4, 254 to 264C: −27 to 0, 33 to 37, 255 to 264D: −27 to 0, 33 to 36, 256 to 264 |
Data for the outermost shell are given in parentheses.
1Bijvoet‐pairs were kept separate for data processing.
2 R merge = 100 ΣhΣi|I h,i— 〈I h〉|/ΣhΣi 〈I h,i〉, where the outer sum (h) is over the unique reflections and the inner sum (i) is over the set of independent observations of each unique reflection.