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 |