7Z3U

Crystal structure of SARS-CoV-2 Main Protease after incubation with Sulfo-Calpeptin

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	2021-05-07
Detector	DECTRIS EIGER2 S 16M
Wavelength(s)	1.033
Spacegroup name	P 21 21 21
Unit cell lengths	67.692, 99.598, 103.261
Unit cell angles	90.00, 90.00, 90.00

Refinement procedure

Resolution	49.220 - 1.720
R-factor	0.1919
Rwork	0.191
R-free	0.23510
Structure solution method	MOLECULAR REPLACEMENT
Starting model (for MR)	6ynq
RMSD bond length	0.013
RMSD bond angle	1.279
Data reduction software	XDS
Data scaling software	XSCALE
Phasing software	PHENIX
Refinement software	PHENIX (1.20.1_4487)

Data quality characteristics

	Overall	Outer shell
Low resolution limit [Å]	49.220	1.782
High resolution limit [Å]	1.720	1.720
Rmerge	0.101	2.172
Rmeas	0.109	2.328
Rpim	0.039	0.828
Number of reflections	74689	7314
<I/σ(I)>	12.54	0.95
Completeness [%]	99.7	98.31
Redundancy	7.5	7.7
CC(1/2)	0.999	0.524

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION		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. Crystals were manually harvested and flash cooled in liquid nitrogen for subsequent X-ray diffraction data collection.