8B56
Crystal structure of SARS-CoV-2 main protease (MPro) in complex with the inhibitor GD-9
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2) |
Synchrotron site | PETRA III, EMBL c/o DESY |
Beamline | P14 (MX2) |
Temperature [K] | 100 |
Detector technology | PIXEL |
Collection date | 2022-03-04 |
Detector | DECTRIS EIGER X 16M |
Wavelength(s) | 0.976250 |
Spacegroup name | P 21 21 21 |
Unit cell lengths | 67.833, 99.107, 102.706 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 56.600 - 1.823 |
R-factor | 0.1872 |
Rwork | 0.185 |
R-free | 0.23140 |
Structure solution method | FOURIER SYNTHESIS |
Starting model (for MR) | 7mbg |
Data reduction software | XDS |
Data scaling software | STARANISO |
Phasing software | PHENIX |
Refinement software | PHENIX (1.20_4459) |
Data quality characteristics
Overall | Outer shell | |
Low resolution limit [Å] | 56.602 | 2.033 |
High resolution limit [Å] | 1.823 | 1.823 |
Rmerge | 0.142 | |
Number of reflections | 40029 | 2001 |
<I/σ(I)> | 11.4 | |
Completeness [%] | 64.1 | |
Redundancy | 13.4 | |
CC(1/2) | 0.999 | 0.572 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, HANGING DROP | 6 | 293.15 | 0.1 M PCTP BUFFER PH 6.0 (PCTP REPRESENTS A MIXTURE OF SODIUM PROPIONATE, SODIUM CACODYLATE TRIHYDRATE, AND BIS-TRIS PROPANE) AND 25% PEG1500 |