7AF0

Structure of SARS-CoV-2 Main Protease bound to Ipidacrine.

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	2020-04-29
Detector	DECTRIS PILATUS3 6M
Wavelength(s)	1.0332
Spacegroup name	C 1 2 1
Unit cell lengths	112.753, 52.960, 44.842
Unit cell angles	90.00, 102.90, 90.00

Refinement procedure

Resolution	27.490 - 1.700
R-factor	0.1792
Rwork	0.178
R-free	0.22500
Structure solution method	MOLECULAR REPLACEMENT
Starting model (for MR)	6yb7
RMSD bond length	0.011
RMSD bond angle	1.428
Data reduction software	XDS
Data scaling software	XSCALE
Phasing software	REFMAC
Refinement software	REFMAC (5.8.0222)

Data quality characteristics

	Overall	Outer shell
Low resolution limit [Å]	27.490	1.761
High resolution limit [Å]	1.700	1.700
Number of reflections	28452	2822
<I/σ(I)>	6.05
Completeness [%]	99.7	99.51
Redundancy	3.5
CC(1/2)	0.993	0.764

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	COUNTER-DIFFUSION		291	Co-crystallization with the compounds was achieved by equilibrating a 6.25 mg/ml protein solution in 20 mM HEPES buffer (pH 7.8) containing 1 mM DTT, 1 mMEDTA, and 150 mM NaCl against a reservoir solution of 100 mM MIB, pH 7.5, containing 25% w/w 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 obtain well-diffracting crystals in a reproducible way seeding was applied for crystal growth. Crystals appeared within a few hours and reached their final size after 2 - 3 days. Crystals were manually harvested and flash-frozen in liquid nitrogen for subsequent X-ray diffraction data collection.