7NEO

Crystal Structure of SARS-CoV-2 main protease (Nsp5) in complex with compound 15

This is a non-PDB format compatible entry.

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	2020-12-20
Detector	DECTRIS EIGER X 16M
Wavelength(s)	0.976
Spacegroup name	P 1 21 1
Unit cell lengths	44.572, 53.822, 114.768
Unit cell angles	90.00, 100.49, 90.00

Refinement procedure

Resolution	48.627 - 1.640
Rwork	0.201
R-free	0.23870
Structure solution method	MOLECULAR REPLACEMENT
Starting model (for MR)	7b2j
RMSD bond length	0.011
RMSD bond angle	1.704
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	Outer shell
Low resolution limit [Å]	48.670	1.670
High resolution limit [Å]	1.640	1.640
Rmerge	0.065	0.431
Rmeas	0.079	0.529
Rpim	0.045	0.302
Number of reflections	65712	3232
<I/σ(I)>	11.3	3.2
Completeness [%]	99.9	100
Redundancy	5.6	5.6
CC(1/2)	0.998	0.940

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