8YBB
Crystal structure of the sigma-1 receptor from Xenopus laevis with side opening
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | SSRF BEAMLINE BL19U1 |
Synchrotron site | SSRF |
Beamline | BL19U1 |
Temperature [K] | 100 |
Detector technology | PIXEL |
Collection date | 2024-01-20 |
Detector | DECTRIS PILATUS3 6M |
Wavelength(s) | 0.97861 |
Spacegroup name | C 1 2 1 |
Unit cell lengths | 86.901, 146.848, 145.804 |
Unit cell angles | 90.00, 107.01, 90.00 |
Refinement procedure
Resolution | 44.815 - 3.120 |
R-factor | 0.237 |
Rwork | 0.235 |
R-free | 0.26710 |
Structure solution method | MOLECULAR REPLACEMENT |
RMSD bond length | 0.002 |
RMSD bond angle | 0.491 |
Data reduction software | XDS (BUILT 20230630) |
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] | 46.476 | 3.048 |
High resolution limit [Å] | 2.808 | 2.808 |
Rmerge | 0.109 | 1.262 |
Rmeas | 0.120 | 1.413 |
Rpim | 0.051 | 0.628 |
Total number of observations | 179405 | 8064 |
Number of reflections | 32257 | 1613 |
<I/σ(I)> | 10.3 | 1.5 |
Completeness [%] | 75.6 | |
Redundancy | 5.6 | 5 |
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 |