7QKA
Crystal structure of SARS-CoV-2 Main Protease in complex with covalently bound GC376
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | PETRA III, DESY BEAMLINE P11 |
Synchrotron site | PETRA III, DESY |
Beamline | P11 |
Temperature [K] | 100 |
Detector technology | PIXEL |
Collection date | 2021-08-14 |
Detector | DECTRIS EIGER2 X 16M |
Wavelength(s) | 1.033 |
Spacegroup name | C 1 2 1 |
Unit cell lengths | 113.675, 53.356, 44.994 |
Unit cell angles | 90.00, 102.51, 90.00 |
Refinement procedure
Resolution | 48.090 - 1.800 |
R-factor | 0.1667 |
Rwork | 0.163 |
R-free | 0.20720 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 7ar6 |
RMSD bond length | 0.013 |
RMSD bond angle | 1.081 |
Data reduction software | XDS |
Data scaling software | XDS |
Phasing software | PHENIX |
Refinement software | PHENIX (1.18-3855_9999) |
Data quality characteristics
Overall | Outer shell | |
Low resolution limit [Å] | 48.090 | 1.864 |
High resolution limit [Å] | 1.800 | 1.800 |
Rmerge | 0.043 | 0.530 |
Rmeas | 0.047 | 0.576 |
Rpim | 0.018 | 0.221 |
Number of reflections | 24372 | 2369 |
<I/σ(I)> | 23.4 | 3.05 |
Completeness [%] | 98.9 | 98.22 |
Redundancy | 6.9 | 6.6 |
CC(1/2) | 1.000 | 0.900 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION | 7.5 | 291 | Co-crystallization with the compound was achieved by equlibrating a 6.25 mg/ml protein solution in 20 mM HEPES buffer (pH 7.8) containing 1 mM DTT, 1mM EDTA, and 150 mM NaCl against a reservoir solution of 100 mM MIB buffer (2:3:3 molar ratio of malonic acid, imidazole, and boric acid), pH 7.5, containing 25% v/v PEG 1500 and 5% v/v DMSO. Prior to crystallization compound solutions in DMSO were dried onto the wells of SwissCI 96-well plates. To achieve reproducible crystal growth seeding was used. Crystals appeared within a few hours and reached their final size after 2 -3 days. |