7B2U
Crystal Structure of SARS-CoV-2 main protease (Nsp5) in complex with compound 1
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 | P 1 21 1 |
Unit cell lengths | 44.517, 53.682, 114.508 |
Unit cell angles | 90.00, 100.59, 90.00 |
Refinement procedure
Resolution | 48.450 - 1.550 |
R-factor | 0.2102 |
Rwork | 0.208 |
R-free | 0.24630 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 7k3t |
RMSD bond length | 0.010 |
RMSD bond angle | 1.076 |
Data reduction software | XDS (b. 20200131) |
Data scaling software | Aimless (0.7.4) |
Phasing software | PHASER (2.8.2) |
Refinement software | PHENIX (1.18.2_3874) |
Data quality characteristics
Overall | Outer shell | |
Low resolution limit [Å] | 53.680 | 1.580 |
High resolution limit [Å] | 1.550 | 1.550 |
Rmerge | 0.060 | 1.110 |
Rmeas | 0.066 | |
Rpim | 0.025 | 0.585 |
Number of reflections | 74540 | 3130 |
<I/σ(I)> | 10.1 | 1.3 |
Completeness [%] | 96.5 | 82.6 |
Redundancy | 6.5 | 4.4 |
CC(1/2) | 0.999 | 0.708 |
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, 10 mM compound, 5% DMSO, 10% PEG300, 20% PEG3K, RT, 2 h. |