7BIJ
Crystal Structure of SARS-CoV-2 main protease (Nsp5) in complex with compound 13
This is a non-PDB format compatible entry.
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 | 2020-12-20 |
Detector | DECTRIS EIGER X 16M |
Wavelength(s) | 0.97625 |
Spacegroup name | C 1 2 1 |
Unit cell lengths | 114.745, 53.839, 44.589 |
Unit cell angles | 90.00, 100.58, 90.00 |
Refinement procedure
Resolution | 33.930 - 1.470 |
Rwork | 0.175 |
R-free | 0.21250 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 7b2j |
RMSD bond length | 0.010 |
RMSD bond angle | 1.799 |
Data reduction software | XDS (b. 20200131) |
Data scaling software | Aimless (0.7.4) |
Phasing software | PHASER (0.7.4) |
Refinement software | REFMAC (5.8.0267) |
Data quality characteristics
Overall | Outer shell | |
Low resolution limit [Å] | 33.930 | 1.500 |
High resolution limit [Å] | 1.470 | 1.470 |
Rmerge | 0.058 | 0.459 |
Rmeas | 0.069 | 0.523 |
Rpim | 0.037 | 0.372 |
Number of reflections | 44811 | 1891 |
<I/σ(I)> | 13.7 | 2.4 |
Completeness [%] | 98.5 | 85.4 |
Redundancy | 6.5 | 4.4 |
CC(1/2) | 0.998 | 0.839 |
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. |