8WS3

Crystal structure of SARS-CoV-2 Main Protease (Mpro) with covalent inhibitor 5,8-Dihydroxy-1,4-naphthoquinone

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	SSRF BEAMLINE BL18U1
Synchrotron site	SSRF
Beamline	BL18U1
Temperature [K]	289
Detector technology	PIXEL
Collection date	2021-12-13
Detector	DECTRIS EIGER X 16M
Wavelength(s)	0.97915
Spacegroup name	C 1 2 1
Unit cell lengths	123.562, 80.994, 63.692
Unit cell angles	90.00, 90.17, 90.00

Refinement procedure

Resolution	24.370 - 2.500
R-factor	0.2144
Rwork	0.210
R-free	0.25240
Structure solution method	MOLECULAR REPLACEMENT
RMSD bond length	0.005
RMSD bond angle	0.866
Data scaling software	HKL-3000
Phasing software	PHENIX
Refinement software	PHENIX (1.20.1)

Data quality characteristics

	Overall	Inner shell	Outer shell
Low resolution limit [Å]	50.000	50.000	2.540
High resolution limit [Å]	2.500	6.780	2.500
Rmerge	0.093	0.065	0.928
Rmeas	0.101	0.071	1.017
Rpim	0.039	0.029	0.408
Total number of observations	141510
Number of reflections	21836	1136	1084
<I/σ(I)>	6.1
Completeness [%]	99.9	99.3	98.5
Redundancy	6.5	6	5.7
CC(1/2)	0.992	0.996	0.815

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, HANGING DROP	6	289	MES pH 6.0, polyethylene glycol (PEG) 6000, DMSO, DTT