8W4D
Crystal structure of the sigma-1 receptor from Xenopus laevis in the absence of known ligands
Experimental procedure
| Experimental method | SINGLE WAVELENGTH |
| Source type | SYNCHROTRON |
| Source details | SSRF BEAMLINE BL18U1 |
| Synchrotron site | SSRF |
| Beamline | BL18U1 |
| Temperature [K] | 100 |
| Detector technology | PIXEL |
| Collection date | 2023-05-19 |
| Detector | DECTRIS PILATUS3 6M |
| Wavelength(s) | 0.97853 |
| Spacegroup name | I 4 3 2 |
| Unit cell lengths | 160.490, 160.490, 160.490 |
| Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
| Resolution | 42.893 - 2.173 |
| R-factor | 0.2137 |
| Rwork | 0.212 |
| R-free | 0.23780 |
| Structure solution method | MOLECULAR REPLACEMENT |
| RMSD bond length | 0.003 |
| RMSD bond angle | 0.639 |
| Data reduction software | XDS (BUILT 20220820) |
| Data scaling software | Aimless (0.7.4) |
| Phasing software | PHASER |
| Refinement software | PHENIX (1.13_2998) |
Data quality characteristics
| Overall | Outer shell | |
| Low resolution limit [Å] | 42.893 | 2.161 |
| High resolution limit [Å] | 2.098 | 2.098 |
| Rmerge | 0.157 | 2.525 |
| Rmeas | 0.162 | 2.595 |
| Rpim | 0.038 | 0.593 |
| Total number of observations | 354050 | 19174 |
| Number of reflections | 20092 | 1007 |
| <I/σ(I)> | 15.1 | 1.4 |
| Completeness [%] | 95.9 | |
| Redundancy | 17.6 | 19 |
Crystallization Conditions
| crystal ID | method | pH | temperature | details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 5.5 | 293.15 | 0.32M LiCl, 0.1M Na+-citrate pH 5.5, 12% PEG 4000, 10% glycerol, 15mM Na+-cholate |
