8W4B
The sigma-1 receptor from Xenopus laevis in complex with progesterone by co-crystallization
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 | 2023-07-03 |
Detector | DECTRIS PILATUS3 6M |
Wavelength(s) | 0.97853 |
Spacegroup name | I 4 3 2 |
Unit cell lengths | 161.196, 161.196, 161.196 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 32.904 - 2.152 |
R-factor | 0.1993 |
Rwork | 0.198 |
R-free | 0.21420 |
Structure solution method | MOLECULAR REPLACEMENT |
RMSD bond length | 0.004 |
RMSD bond angle | 0.784 |
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] | 43.081 | 2.148 |
High resolution limit [Å] | 2.105 | 2.105 |
Rmerge | 0.126 | 2.747 |
Rmeas | 0.129 | 2.825 |
Rpim | 0.027 | 0.656 |
Total number of observations | 460385 | 17995 |
Number of reflections | 20044 | 980 |
<I/σ(I)> | 14.6 | 1.1 |
Completeness [%] | 95.5 | |
Redundancy | 23 | 18.4 |
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, 1mM progesterone |