7AVD

Structure of SARS-CoV-2 Main Protease bound to SEN1269 ligand

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	2020-04-02
Detector	DECTRIS PILATUS 6M
Wavelength(s)	1.0332
Spacegroup name	P 1 21 1
Unit cell lengths	44.552, 53.857, 114.731
Unit cell angles	90.00, 100.61, 90.00

Refinement procedure

Resolution	48.600 - 1.800
R-factor	0.1964
Rwork	0.194
R-free	0.23870
Structure solution method	MOLECULAR REPLACEMENT
Starting model (for MR)	6yb7
Data reduction software	XDS
Data scaling software	XSCALE
Phasing software	PHASER
Refinement software	PHENIX (1.18-3855_9999)

Data quality characteristics

	Overall	Outer shell
Low resolution limit [Å]	112.770	1.840
High resolution limit [Å]	1.800	1.800
Rmerge	0.157	1.490
Rmeas	0.182
Rpim	0.092	0.860
Number of reflections	49485	2906
<I/σ(I)>	5.6	0.9
Completeness [%]	99.5	99.5
Redundancy	3.8	3.9
CC(1/2)	0.995	0.408

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	COUNTER-DIFFUSION	7.5	291	Co-crystallization with the compounds 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.