7AMJ

Structure of SARS-CoV-2 Main Protease bound to PD 168568.

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	2020-04-05
Detector	DECTRIS PILATUS 6M-F
Wavelength(s)	1.0332
Spacegroup name	C 1 2 1
Unit cell lengths	112.682, 52.928, 44.714
Unit cell angles	90.00, 102.89, 90.00

Refinement procedure

Resolution	54.920 - 1.590
R-factor	0.1748
Rwork	0.173
R-free	0.21040
Structure solution method	MOLECULAR REPLACEMENT
Starting model (for MR)	6ynq
RMSD bond length	0.007
RMSD bond angle	0.723
Data reduction software	DIALS
Data scaling software	DIALS
Phasing software	PHASER
Refinement software	REFMAC (5.8.0222)

Data quality characteristics

	Overall	Outer shell
Low resolution limit [Å]	54.920	1.620
High resolution limit [Å]	1.590	1.590
Rmerge	0.092	0.668
Rmeas	0.108	0.788
Rpim	0.056	0.411
Number of reflections	34590	1683
<I/σ(I)>	6.4	1.3
Completeness [%]	99.8	97.5
Redundancy	3.6	3.4
CC(1/2)	0.994	0.453

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.