7NEV

Structure of the hemiacetal complex between the SARS-CoV-2 Main Protease and Leupeptin

Replaces:  6YZ6

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	2020-04-09
Detector	DECTRIS PILATUS3 6M
Wavelength(s)	1.0332
Spacegroup name	C 1 2 1
Unit cell lengths	113.811, 52.682, 46.230
Unit cell angles	90.00, 102.78, 90.00

Refinement procedure

Resolution	23.800 - 1.700
R-factor	0.1856
Rwork	0.183
R-free	0.23360
Structure solution method	MOLECULAR REPLACEMENT
Starting model (for MR)	6ynq
RMSD bond length	0.002
RMSD bond angle	0.561
Data reduction software	XDS
Data scaling software	DIALS
Phasing software	PHENIX
Refinement software	PHENIX (1.19_4092)

Data quality characteristics

	Overall	Outer shell
Low resolution limit [Å]	31.280	1.730
High resolution limit [Å]	1.690	1.690
Rmerge	0.067	0.528
Number of reflections	29274	2106
<I/σ(I)>	10.2	1.7
Completeness [%]	97.7	96.5
Redundancy	3.7	3.7
CC(1/2)	0.995	0.530

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR 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.