7QKA

Crystal structure of SARS-CoV-2 Main Protease in complex with covalently bound GC376

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	2021-08-14
Detector	DECTRIS EIGER2 X 16M
Wavelength(s)	1.033
Spacegroup name	C 1 2 1
Unit cell lengths	113.675, 53.356, 44.994
Unit cell angles	90.00, 102.51, 90.00

Refinement procedure

Resolution	48.090 - 1.800
R-factor	0.1667
Rwork	0.163
R-free	0.20720
Structure solution method	MOLECULAR REPLACEMENT
Starting model (for MR)	7ar6
RMSD bond length	0.013
RMSD bond angle	1.081
Data reduction software	XDS
Data scaling software	XDS
Phasing software	PHENIX
Refinement software	PHENIX (1.18-3855_9999)

Data quality characteristics

	Overall	Outer shell
Low resolution limit [Å]	48.090	1.864
High resolution limit [Å]	1.800	1.800
Rmerge	0.043	0.530
Rmeas	0.047	0.576
Rpim	0.018	0.221
Number of reflections	24372	2369
<I/σ(I)>	23.4	3.05
Completeness [%]	98.9	98.22
Redundancy	6.9	6.6
CC(1/2)	1.000	0.900

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION	7.5	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.