7Z3U
Crystal structure of SARS-CoV-2 Main Protease after incubation with Sulfo-Calpeptin
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 | 2021-05-07 |
Detector | DECTRIS EIGER2 S 16M |
Wavelength(s) | 1.033 |
Spacegroup name | P 21 21 21 |
Unit cell lengths | 67.692, 99.598, 103.261 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 49.220 - 1.720 |
R-factor | 0.1873 |
Rwork | 0.186 |
R-free | 0.21560 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 6ynq |
RMSD bond length | 0.006 |
RMSD bond angle | 0.922 |
Data reduction software | XDS |
Data scaling software | XSCALE |
Phasing software | PHENIX |
Refinement software | PHENIX (1.18-3855_9999) |
Data quality characteristics
Overall | Outer shell | |
Low resolution limit [Å] | 49.220 | 1.782 |
High resolution limit [Å] | 1.720 | 1.720 |
Rmerge | 0.101 | 2.172 |
Rmeas | 0.109 | 2.328 |
Rpim | 0.039 | 0.828 |
Number of reflections | 74689 | 7314 |
<I/σ(I)> | 12.54 | 0.95 |
Completeness [%] | 99.7 | 98.31 |
Redundancy | 7.5 | 7.7 |
CC(1/2) | 0.999 | 0.524 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION | 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. Crystals were manually harvested and flash cooled in liquid nitrogen for subsequent X-ray diffraction data collection. |