7AEG
SARS-CoV-2 main protease in a covalent complex with SDZ 224015 derivative, compound 5
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | DIAMOND BEAMLINE I24 |
Synchrotron site | Diamond |
Beamline | I24 |
Temperature [K] | 100 |
Detector technology | PIXEL |
Collection date | 2020-07-29 |
Detector | DECTRIS PILATUS 6M-F |
Wavelength(s) | 0.999 |
Spacegroup name | C 1 2 1 |
Unit cell lengths | 112.871, 52.939, 45.526 |
Unit cell angles | 90.00, 103.05, 90.00 |
Refinement procedure
Resolution | 54.980 - 1.700 |
R-factor | 0.166 |
Rwork | 0.164 |
R-free | 0.20210 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 5r8t |
RMSD bond length | 0.006 |
RMSD bond angle | 1.375 |
Data reduction software | DIALS |
Data scaling software | Aimless (0.7.4) |
Phasing software | MOLREP |
Refinement software | REFMAC (5.8.0267) |
Data quality characteristics
Overall | Inner shell | Outer shell | |
Low resolution limit [Å] | 54.980 | 54.980 | 1.730 |
High resolution limit [Å] | 1.700 | 9.000 | 1.700 |
Rmerge | 0.224 | 0.070 | 2.927 |
Rmeas | 0.245 | 0.077 | 3.227 |
Rpim | 0.099 | 0.031 | 1.336 |
Total number of observations | 178201 | 1267 | 9197 |
Number of reflections | 28892 | 214 | 1522 |
<I/σ(I)> | 7.6 | 14.7 | 2.3 |
Completeness [%] | 99.9 | 99.7 | 99.8 |
Redundancy | 6.2 | 5.9 | 6 |
CC(1/2) | 0.985 | 0.996 | 0.301 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 6.5 | 293 | Mpro was thawed and diluted to 6 mg/ml using 20 mM Hepes pH 7.5, 50 mM NaCl. The ligand of interest was dissolved in DMSO to 10 mM and then diluted into the protein solution to a final concentration of 1 mM. The ligand was then allowed to incubate with the protein for two hours at room temperature prior to dispensing plates. The drop composition was 0.15 ul protein ligand solution, 0.3 ul 11% (v/v) PEG 4K, 0.1 M MES pH 6.5, and 0.05 ul Mpro crystal seed stock. The Mpro crystal seed stock was prepared by crushing Mpro crystals with a pipette tip, suspending them in 30% PEG 4K, 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). Reservoir solution was 11pc (v/v) PEG 4K, 5pc (v/v) DMSO, 0.1 M MES pH 6.5. Crystals were grown using the sitting drop vapor diffusion method at 20 degrees C and appeared within 24 hours, reaching full size within 36 hours. |