7O46

Crystal Structure of SARS-CoV-2 main protease (Nsp5) in complex with compound 17

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)	0.976
Spacegroup name	C 1 2 1
Unit cell lengths	113.666, 54.064, 44.931
Unit cell angles	90.00, 101.47, 90.00

Refinement procedure

Resolution	34.180 - 2.230
R-factor	0.1984
Rwork	0.196
R-free	0.24870
Structure solution method	MOLECULAR REPLACEMENT
Starting model (for MR)	7b5z
RMSD bond length	0.007
RMSD bond angle	1.507
Data reduction software	XDS (b. 20200131)
Data scaling software	Aimless (0.7.4)
Phasing software	PHASER (2.8.2)
Refinement software	REFMAC (5.8.0267)

Data quality characteristics

	Overall	Inner shell	Outer shell
Low resolution limit [Å]	48.640	48.640	2.310
High resolution limit [Å]	2.230	8.640	2.230
Rmerge	0.055	0.040	1.443
Rmeas	0.059	0.045	1.560
Rpim	0.023	0.019	0.587
Total number of observations	89181	1359	8644
Number of reflections	13122	236	1242
<I/σ(I)>	14.6	37.4	1.4
Completeness [%]	99.7	95.5	97.7
Redundancy	6.8	5.8	7
CC(1/2)	0.998	0.997	0.537

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% PEG3K, RT, 2 h.