7B2J

Crystal Structure of SARS-CoV-2 main protease (Nsp5) in complex with compound 5

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	MAX IV BEAMLINE BioMAX
Synchrotron site	MAX IV
Beamline	BioMAX
Temperature [K]	100
Detector technology	PIXEL
Collection date	2020-11-12
Detector	DECTRIS EIGER X 16M
Wavelength(s)	0.976
Spacegroup name	C 1 2 1
Unit cell lengths	114.548, 53.652, 44.568
Unit cell angles	90.00, 100.56, 90.00

Refinement procedure

Resolution	48.440 - 1.550
R-factor	0.1635
Rwork	0.162
R-free	0.20260
Structure solution method	MOLECULAR REPLACEMENT
Starting model (for MR)	7k3t
RMSD bond length	0.008
RMSD bond angle	1.325
Data reduction software	XDS (b. 20200131)
Data scaling software	Aimless (0.7.4)
Phasing software	PHASER (2.8.2)
Refinement software	REFMAC (5)

Data quality characteristics

	Overall	Outer shell
Low resolution limit [Å]	48.440	1.580
High resolution limit [Å]	1.550	1.550
Rmerge	0.067	0.722
Rmeas	0.073	0.819
Rpim	0.028	0.377
Number of reflections	37807	1554
<I/σ(I)>	13.2	2.1
Completeness [%]	97.8	81.4
Redundancy	6.5	4.4
CC(1/2)	0.999	0.727

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP	7.75	293	100 nL protein (8.3 mg/mL, 50 mM Tris pH 8.0, 300 mM NaCl), 50 nL seeds, 450 nL reservoir (200 mM HEPES pH 7.75, 5% DMSO, 12.5% PEG4K). Soaking: 200 mM HEPES pH 7.75, 15 mM compound, 7.5% DMSO, 10% PEG300, 20% PEG3K, RT, 2 h.