7B77
Crystal Structure of SARS-CoV-2 main protease (Nsp5) in complex with compound 8
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | MAX IV BEAMLINE BioMAX |
Synchrotron site | MAX IV |
Beamline | BioMAX |
Temperature [K] | 100 |
Detector technology | PIXEL |
Collection date | 2020-11-12 |
Detector | DECTRIS EIGER X 16M |
Wavelength(s) | 0.976 |
Spacegroup name | C 1 2 1 |
Unit cell lengths | 114.539, 53.602, 44.570 |
Unit cell angles | 90.00, 100.50, 90.00 |
Refinement procedure
Resolution | 43.820 - 1.600 |
R-factor | 0.1708 |
Rwork | 0.169 |
R-free | 0.21380 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 7b2j |
RMSD bond length | 0.008 |
RMSD bond angle | 1.128 |
Data reduction software | XDS (b. 20200131) |
Data scaling software | Aimless (0.7.4) |
Phasing software | PHASER (2.8.2) |
Refinement software | REFMAC (5.8.0267) |
Data quality characteristics
Overall | Outer shell | |
Low resolution limit [Å] | 48.400 | 1.630 |
High resolution limit [Å] | 1.600 | 1.600 |
Rmerge | 0.055 | 0.420 |
Rmeas | 0.065 | 0.534 |
Rpim | 0.035 | 0.324 |
Number of reflections | 34900 | 1587 |
<I/σ(I)> | 15 | 3.2 |
Completeness [%] | 99.3 | 92.5 |
Redundancy | 6.6 | 4.9 |
CC(1/2) | 0.999 | 0.931 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.75 | 293 | 100 nL protein (8.3 mg/mL, 50 mM Tris pH 8.0, 300 mM NaCl), 50 nL seeds, 450 nL reservoir (200 mM HEPES pH 7.75, 5% DMSO, 12.5% PEG4K). Soaking: 200 mM HEPES pH 7.75, 12.5 mM compound, 5% DMSO, 10% PEG300, 20% PEG3K, RT, 2 h. |