7AEH

SARS-CoV-2 main protease in a covalent complex with a pyridine derivative of ABT-957, compound 1

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	DIAMOND BEAMLINE I04-1
Synchrotron site	Diamond
Beamline	I04-1
Temperature [K]	100
Detector technology	PIXEL
Collection date	2020-06-12
Detector	DECTRIS PILATUS 6M-F
Wavelength(s)	0.9126
Spacegroup name	C 1 2 1
Unit cell lengths	113.954, 53.080, 44.546
Unit cell angles	90.00, 103.02, 90.00

Refinement procedure

Resolution	47.930 - 1.300
R-factor	0.14
Rwork	0.138
R-free	0.17350
Structure solution method	MOLECULAR REPLACEMENT
Starting model (for MR)	5r8t
RMSD bond length	0.007
RMSD bond angle	1.412
Data reduction software	DIALS
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]	55.510	55.510	1.320
High resolution limit [Å]	1.300	6.990	1.300
Rmerge	0.199	0.069	6.011
Rmeas	0.209	0.073	6.402
Rpim	0.066	0.023	2.163
Total number of observations	627154	4287	25324
Number of reflections	62149	436	2913
<I/σ(I)>	10.7	27.6	1.9
Completeness [%]	97.2	99.7	88.7
Redundancy	10.1	9.8	8.7
CC(1/2)	0.996	0.992	0.310

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.