7AGA

Structure of SARS-CoV-2 Main Protease bound to AT7519

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	2020-04-28
Detector	DECTRIS PILATUS 6M-F
Wavelength(s)	1.003
Spacegroup name	C 1 2 1
Unit cell lengths	112.372, 52.641, 44.585
Unit cell angles	90.00, 102.67, 90.00

Refinement procedure

Resolution	30.930 - 1.680
R-factor	0.1877
Rwork	0.186
R-free	0.22250
Structure solution method	MOLECULAR REPLACEMENT
Starting model (for MR)	6yb7
RMSD bond length	0.009
RMSD bond angle	0.761
Data reduction software	XDS
Data scaling software	XDS
Phasing software	PHASER
Refinement software	PHENIX (1.13-2998_9999)

Data quality characteristics

	Overall	Outer shell
Low resolution limit [Å]	30.930	1.780
High resolution limit [Å]	1.680	1.680
Number of reflections	28529	4605
<I/σ(I)>	9.01	0.62
Completeness [%]	97.8	99.6
Redundancy	3.7	3.7
CC(1/2)	0.998	0.231

Crystallization Conditions

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