7AQI

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

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	2020-04-06
Detector	DECTRIS PILATUS 6M
Wavelength(s)	1.0332
Spacegroup name	C 1 2 1
Unit cell lengths	113.185, 52.987, 44.688
Unit cell angles	90.00, 103.02, 90.00

Refinement procedure

Resolution	47.810 - 1.700
R-factor	0.2273
Rwork	0.226
R-free	0.26560
Structure solution method	MOLECULAR REPLACEMENT
Starting model (for MR)	6yb7
Data reduction software	XDS
Data scaling software	XSCALE
Phasing software	PHASER
Refinement software	REFMAC (5.8)

Data quality characteristics

	Overall	Outer shell
Low resolution limit [Å]	47.810	1.761
High resolution limit [Å]	1.700	1.700
Rmerge		0.847
Rmeas		0.992
Number of reflections	28082	2719
<I/σ(I)>	4.35	0.95
Completeness [%]	98.5	96.59
Redundancy	3.6	3.7
CC(1/2)	0.992	0.222

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.