7B5Z

Crystal Structure of SARS-CoV-2 main protease (Nsp5) in complex with compound 6

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	114.457, 53.656, 44.476
Unit cell angles	90.00, 100.51, 90.00

Refinement procedure

Resolution	48.430 - 1.650
R-factor	0.1573
Rwork	0.155
R-free	0.19610
Structure solution method	MOLECULAR REPLACEMENT
Starting model (for MR)	7b2j
RMSD bond length	0.015
RMSD bond angle	1.584
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]	48.430	1.680
High resolution limit [Å]	1.650	1.650
Rmerge	0.058	0.335
Rmeas	0.063	0.368
Rpim	0.025	0.148
Number of reflections	31557	1437
<I/σ(I)>	18.6	5.2
Completeness [%]	98.6	92.9
Redundancy	6.5	6
CC(1/2)	0.999	0.948

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, 12.5 mM compound, 5% DMSO, 10% PEG300, 20% PEG3K, RT, 2 h.