Table 1 Data collection and refinement statistics.
bR dark (5J7A; this work) | bR 1 ms (this work) | SMX (4X31) | Cryo (4X32) | |
|---|---|---|---|---|
Data collection | ||||
X-ray source | CXI, LCLS | CXI, LCLS | ID13, ESRF | PXI-X06SA, SLS |
Detector | CSPAD | CSPAD | Rayonix MX-170 CCD | PILATUS 6 M |
Temperature (K) | 294 | 294 | 294 | 100 |
Wavelength (Å) | 1.83 | 1.83 | 0.954 | 1.000 |
Beam size (μm) | 1.5 × 1.5 | 1.5 × 1.5 | 2 × 3 | 50 × 10 |
Average crystal size (μm) | 3–15 × 3–15 × 1–3 | 3–15 × 3–15 × 1–3 | 5–40 × 5–40 × 1–5 | 50 × 50 × 10 |
Pulse duration/no. of photons | 75 fs (nominal)/6.57e10 | 75 fs (nominal)/6.57e10 | 25 ms | 150 ms per image |
Space group | P63 | P63 | P63 | P63 |
Unit cell parameters (Å) | a=b=62.62 c=111.3 | a=b=62.71 c=111.2 | a=b=62.8, c=109.7 | a=b=60.5, c=101.5 |
Indexed images | 13,804 | 7,820 | 5,691 | 2,532 |
Crystals merged | 13,132 | 7,117 | 5,691 | 1 |
Total/unique reflections | 1,799,769/11027 | 714,736/10,981 | 1,223,766/9,655 | 234,541/16,643 |
Resolution range (Å) | 21.9−2.30 (2.41−2.30) | 21.9−2.30 (2.41−2.30) | 36.56−2.40 (2.46−2.40) | 46.57−1.90 (1.94−1.90) |
Completeness (%) | 99.98 (99.86) | 99.36 (92.83) | 100.0 (100.0) | 100.0 (100.0) |
Multiplicity | 163 (16.8) | 65.1 (4.9) | 127 (88.8) | 14.1 (14.3) |
〈I/σ(I)〉 | 6.56 (1.58) | 4.88 (1.56) | 3.57 (1.16) | 17.90 (1.80) |
CC* | 0.998 (0.862) | 0.998 (0.761) | 0.981 (0.658) | 1.000 (0.841) |
Rsplit† (%) or Rp.i.m. (cryo; %) | 11.5 (66.3) | 9.52 (87.4) | 22.4 (107) | 2.6 (50) |
Matthews coefficient° VM (Å3 Da−1) | 2.44 | 2.44 | 2.50 | 2.21 |
Solvent content (%) | 49.65 | 49.65 | 50.76 | 44.27 |
B factor Wilson plot (Å2) | 31.3 | 72.0 | 45.2 | 33.4 |
Refinement | ||||
Resolution range (Å) | 21.66−2.3 (2.36−2.30) | 31.40−2.40 (2.46−2.40) | 52.42−1.90 (1.95−1.90) | |
No. of reflections (total/test set) | 10,660/650 | 9,192/441 | 15,773/841 | |
Rwork/Rfree (%) | 19.0/22.0 | 20.5/24.9 | 17.1/21.4 | |
No. of atoms | ||||
Overall | 1,805 | 1,848 | 1,877 | |
Protein | 1,711 | 1,756 | 1,723 | |
Retinal | 20 | 20 | 20 | |
Water | 17 | 10 | 30 | |
Lipids and other | 57 | 62 | 104 | |
Average B factors (Å2) | ||||
Overall | 19.19 | 40.47 | 28.50 | |
Protein | 17.88 | 39.04 | 27.11 | |
Retinal | 16.13 | 52.67 | 24.61 | |
Water | 43.31 | 55.94 | 36.52 | |
Lipids and other | 52.39 | 74.47 | 49.93 | |
r.m.s.d.’s | ||||
Bond lengths (Å) | 0.008 | 0.008 | 0.009 | |
Bond angles (°) | 1.15 | 1.01 | 1.21 | |
Ramachandran favoured (%) | 99.1 | 98.2 | 98.9 | |
Ramachandran outliers (%) | 0.0 | 0.4 | 0.0 | |
