Table 1. Data collection and refinement statistics.
PDB code | 5G28* (type A crystal) | 5G54* (type B crystal) | 5G2A* (Br ion crystal) | 5G2D* (T102N) | 5G2C* (T102D) |
---|---|---|---|---|---|
Data collection | |||||
Space group | C121 | C121 | C121 | C121 | C121 |
a, b, c (Å) | 102.76, 49.40, 69.33 | 102.72, 49.43, 77.03 | 102.77, 48.85, 69.36 | 103.25, 49.45, 78.40 | 103.44, 50.03, 77.79 |
α, β, γ (°) | 90, 109.85, 90 | 90, 131.16, 90 | 90, 110.13, 90 | 90, 131.89, 90 | 90, 131.47, 90 |
Resolution (Å) | 65.21–1.57 (1.62–1.57)† | 40.00–2.0 (2.05–2.0)† | 65.13–2.17 (2.21–2.17)† | 58.36–1.80 (1.83–1.80)† | 58.28–2.31 (2.34–2.31)† |
Rmerge (%) | 11.1 (65.9)† | 10.2 (69.3)† | 5.9 (20.9)† | 7.0 (39.3)† | 6.0 (31.3)† |
I/σI | 30.81 (4.23)† | 11.1 (1.65)† | 35.46 (7.59)† | 22.67 (2.57)† | 14.43 (1.86)† |
Completeness (%) | 97.4 (93.06)† | 99.3 (96.4)† | 99.0 (98.8)† | 97.1 (81.9)† | 94.5 (73.5)† |
Redundancy | 4.4 (2.7)† | 5.6 (4.9)† | 5.8 (3.9)† | 4.6 (2.4)† | 4.3 (2.0)† |
Refinement | |||||
Resolution (Å) | 65.21–1.57 | 40.0–2.0 | 65.13–2.17 | 58.36–1.80 | 58.28–2.31 |
No. of reflections | 42,520 | 18,695 | 16,316 | 25,345 | 11,889 |
Rwork/Rfree (%) | 15.40/19.38 | 17.60/22.52 | 15.31/20.71 | 17.51/20.52 | 19.45/23.88 |
No. of atoms | |||||
Protein | 2,072 | 2,105 | 2,072 | 2,095 | 2,101 |
Retinal | 20 | 20 | 20 | 20 | 20 |
Water | 136 | 84 | 59 | 93 | 15 |
Lipid fragments | 99 | 101 | — | 108 | 108 |
Chloride | 2 | 2 | 2 | 2 | 1 |
B factors (Å2) | |||||
Protein | 23.82 | 19.03 | 29.22 | 22.87 | 29.27 |
Retinal | 15.57 | 11.06 | 21.66 | 17.02 | 22.14 |
Water | 39.86 | 34.65 | 40.69 | 40.63 | 37.52 |
Lipid fragments | 48.21 | 44.54 | — | 48.38 | 47.48 |
Chloride ions | 32.77 | 38.75 | Br− (67.85) | 40.97 | 58.43 |
r.m.s. deviations | |||||
Bond lengths (Å) | 0.026 | 0.018 | 0.021 | 0.023 | 0.019 |
Bond angles (°) | 1.92 | 1.98 | 1.83 | 1.90 | 1.91 |
Crystal size (μm) | 50 × 50 × 50 | 30 × 30 × 30 | 50 × 50 × 50 | 50 × 50 × 50 | 50 × 50 × 50 |
Radiation dose (MGy) | 0.04 | 0.12 | 0.04 | 0.04 | 0.04 |
PDB, Protein Data Bank; r.m.s., root mean squared.
*Number of crystal used for data collection: 1.
†Highest-resolution shell is shown in parenthesis.