7QBB

Crystal Structure of SARS-CoV-2 main protease (Nsp5) in complex with compound 18

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	2021-02-23
Detector	DECTRIS EIGER X 16M
Wavelength(s)	0.97625
Spacegroup name	C 1 2 1
Unit cell lengths	113.768, 53.821, 44.992
Unit cell angles	90.00, 101.46, 90.00

Refinement procedure

Resolution	48.470 - 2.000
R-factor	0.2096
Rwork	0.207
R-free	0.25800
Structure solution method	MOLECULAR REPLACEMENT
Starting model (for MR)	7b2j
RMSD bond length	0.006
RMSD bond angle	1.435
Data reduction software	XDS (b. 20200131)
Data scaling software	Aimless (0.7.4)
Phasing software	PHASER (0.7.4)
Refinement software	REFMAC (5.8.0267)

Data quality characteristics

	Overall	Inner shell	Outer shell
Low resolution limit [Å]	48.470	48.470	2.070
High resolution limit [Å]	2.000	7.750	2.000
Rmerge	0.070	0.046	1.790
Rmeas	0.076	0.052	1.937
Rpim	0.030	0.022	0.733
Total number of observations	122406	1882	11897
Number of reflections	18097	317	1754
<I/σ(I)>	11.9	31.8	1.1
Completeness [%]	99.7	96	98.3
Redundancy	6.8	5.9	6.8
CC(1/2)	0.997	0.994	0.534

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, 6.25 mM compound, 5% DMSO, 10% PEG300, 20% PEG4K, RT, 2 h.