Table 1 Data collection and refinement statistics for the xlσ1R structures.
From: An open-like conformation of the sigma-1 receptor reveals its ligand entry pathway
xlσ1Rclosed-endo | xlσ1Rclosed-PRE084 | xlσ1Rclosed-S1RA | xlσ1Ropen-endo | xlσ1Ropen-PRE084-co | xlσ1Ropen-PRE084-soak | xlσ1RC179/C203-S1RA | |
|---|---|---|---|---|---|---|---|
PDB ID | 7W2B | 7W2C | 7W2D | 7W2E | 7W2F | 7W2G | 7W2H |
Data collection | |||||||
Space group | P 1 21 1 | P 1 21 1 | P 1 21 1 | P 21 21 21 | P 21 21 21 | P 21 21 21 | P 1 21 1 |
Wavelength (Å) | 0.9793 | 0.9792 | 0.9792 | 0.9793 | 0.9792 | 0.9785 | 0.9785 |
Unit cell | |||||||
a, b, c (Å) | 86.7, 148.5, 172.1 | 87.2, 148.8, 172.8 | 86.3, 147.9, 171.4 | 135.1, 161.5, 200.2 | 135.3, 161.0, 202.2 | 135.0, 161.0, 201.9 | 134.5, 200.8, 160.6 |
α, β, γ (°) | 90, 92.4, 90 | 90, 92.8, 90 | 90, 91.7, 90 | 90, 90, 90 | 90, 90, 90 | 90, 90, 90 | 90, 90.1, 90 |
Resolution (Å) | 3.20 (3.26-3.20) | 3.33 (3.39-3.33) | 3.47 (3.53-3.47) | 3.56 (3.62-3.56) | 3.10 (3.15-3.10) | 2.85 (2.90-2.85) | 3.80 (3.86-3.80) |
Unique reflections | 70,446 (3533) | 59,588 (3209) | 53,754 (2755) | 51,558 (2562) | 80,396 (3993) | 102,980 (5102) | 67,737 (3410) |
Multiplicity | 6.9 (7.2) | 6.6 (6.3) | 3.4 (3.3) | 4.6 (4.6) | 5.2 (5.4) | 11.2 (11.6) | 2.6 (2.4) |
Completeness (%) | 98.3 (100.0) | 92.8 (100.0) | 96.5 (99.9) | 97.4 (98.2) | 99.5 (99.8) | 99.9 (100.0) | 81.1 (81.9) |
I/σI | 12.2 (2.0) | 11.2 (2.4) | 6.7 (1.7) | 7.7 (1.8) | 8.1 (1.6) | 13.3 (1.8) | 4.8 (1.9) |
Rmerge | 0.137 (1.129) | 0.146 (0.859) | 0.147 (0.786) | 0.141 (0.754) | 0.135 (0.931) | 0.134 (1.505) | 0.159 (0.431) |
Rmeas | 0.148 (1.216) | 0.159 (0.932) | 0.175 (0.942) | 0.158 (0.843) | 0.151 (1.033) | 0.140 (1.574) | 0.188 (0.465) |
Rpim | 0.056 (0.450) | 0.061 (0.360) | 0.094 (0.513) | 0.069 (0.367) | 0.065 (0.441) | 0.041 (0.457) | 0.110 (0.313) |
CC1/2 | 0.996 (0.735) | 0.993 (0.780) | 0.988 (0.652) | 0.998 (0.822) | 0.998 (0.774) | 0.999 (0.808) | 0.989 (0.853) |
Refinement | |||||||
Resolution (Å) | 3.20 (3.25–3.20) | 3.33 (3.39–3.33) | 3.47 (3.53–3.47) | 3.56 (3.62–3.56) | 3.10 (3.14–3.10) | 2.85 (2.88–2.85) | 3.80 (3.85–3.80) |
No. reflections | 70,305 | 59,445 | 53,659 | 51,418 | 80,119 | 102,713 | 67,528 |
Completeness (%) | 98.1 | 92.6 | 96.3 | 97.1 | 99.2 | 99.6 | 80.8 |
Rwork/Rfree (%) | 24.1/26.9 | 22.9/25.9 | 23.9/26.7 | 26.4/29.7 | 25.6/28.8 | 25.4/28.3 | 28.3/31.8 |
No. of atoms | 20,673 | 20,833 | 20,593 | 20,974 | 20,904 | 20,822 | 40,341 |
Protein | 20,469 | 20,472 | 20,269 | 20,959 | 20,333 | 20,224 | 39,716 |
Ligands | 204 | 360 | 324 | 416 | 416 | 625 | |
Solvent | 1 | 15 | 155 | 182 | |||
Average B-factor | 85.73 | 91.87 | 104.5 | 101.3 | 80.54 | 76.89 | 82.30 |
Protein | 85.83 | 91.91 | 104.7 | 101.3 | 80.40 | 76.90 | 82.36 |
Ligands | 75.06 | 89.49 | 92.28 | 95.84 | 82.54 | 78.22 | |
Solvent | 58.30 | 76.80 | 58.11 | 63.23 | |||
Ramachandran | |||||||
Favored (%) | 98.01 | 97.39 | 99.01 | 98.60 | 98.59 | 98.98 | 97.72 |
Allowed (%) | 1.99 | 2.61 | 0.91 | 1.40 | 1.41 | 1.02 | 2.24 |
Outliers (%) | 0.00 | 0.00 | 0.08 | 0.00 | 0.00 | 0.00 | 0.04 |
RMS bonds (Å) | 0.002 | 0.002 | 0.002 | 0.003 | 0.002 | 0.003 | 0.002 |
RMS angles (°) | 0.537 | 0.495 | 0.575 | 0.559 | 0.449 | 0.694 | 0.456 |
Clashscore | 3.50 | 3.04 | 4.97 | 4.82 | 4.16 | 3.72 | 4.28 |
