7Z59
SARS-CoV-2 main protease (Mpro) covalently modified with a penicillin derivative
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | DIAMOND BEAMLINE I03 |
Synchrotron site | Diamond |
Beamline | I03 |
Temperature [K] | 100 |
Detector technology | PIXEL |
Collection date | 2021-12-11 |
Detector | DECTRIS EIGER X 16M |
Wavelength(s) | 0.97625 |
Spacegroup name | C 1 2 1 |
Unit cell lengths | 113.341, 53.808, 44.703 |
Unit cell angles | 90.00, 100.65, 90.00 |
Refinement procedure
Resolution | 55.695 - 2.000 |
Rwork | 0.222 |
R-free | 0.25160 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 6yb7 |
RMSD bond length | 0.008 |
RMSD bond angle | 1.481 |
Data reduction software | xia2 |
Data scaling software | Aimless |
Phasing software | MOLREP |
Refinement software | REFMAC (5.8.0267) |
Data quality characteristics
Overall | Inner shell | Outer shell | |
Low resolution limit [Å] | 55.695 | 55.690 | 2.050 |
High resolution limit [Å] | 2.000 | 8.940 | 2.000 |
Rmerge | 0.188 | 0.047 | 4.066 |
Rmeas | 0.208 | 0.051 | 4.490 |
Rpim | 0.088 | 0.021 | 1.893 |
Number of reflections | 18025 | 2192 | 14239 |
<I/σ(I)> | 7.9 | ||
Completeness [%] | 100.0 | 100 | 100 |
Redundancy | 10.7 | 10.1 | 10.8 |
CC(1/2) | 0.997 | 0.998 | 0.211 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 6 | 293 | SARS-CoV-2 Mpro was thawed and diluted to 6 mg/mL (using 20 mM HEPES, pH 7.5, 50 mM NaCl). Beta-Lactam 20e was added to the protein solution to a final concentration of 10 mM; the mixture was incubated for 2 h at ambient temperature prior to dispensing plates. The drop composition was 0.15 uL protein ligand solution, 0.3 uL 11 percent v/v PEG 4000, 0.1 M MES, pH 6.5, and 0.05 ,microL Mpro crystal seed stock. The Mpro crystal seed stock was prepared by crushing Mpro crystals with a pipette tip, suspending them in 30% PEG 4000, 5%v/v DMSO, 0.1 M MES pH 6.5, and vortexing for 60 s with approximately 10 glass beads (1.0 mm diameter, BioSpec products). As reservoir solution was used: 11%v/v PEG 4K, 5%v/v DMSO, 0.1 M MES, pH 6.5. Crystals were grown using the sitting drop vapor diffusion method at 20 degree C and appeared within 24 h, reaching full size within 36 h. Crystals were looped after one week. |