7NBT

Crystal Structure of SARS-CoV-2 main protease (Nsp5) in complex with compound 21

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)	0.97625
Spacegroup name	C 1 2 1
Unit cell lengths	114.582, 53.770, 44.524
Unit cell angles	90.00, 100.53, 90.00

Refinement procedure

Resolution	43.813 - 1.630
Rwork	0.190
R-free	0.23020
Structure solution method	MOLECULAR REPLACEMENT
Starting model (for MR)	7b2j
RMSD bond length	0.008
RMSD bond angle	1.552
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]	56.330	1.660
High resolution limit [Å]	1.630	1.630
Rmerge	0.060	0.747
Rmeas	0.074	0.932
Rpim	0.043	0.550
Number of reflections	32705	1649
<I/σ(I)>	11.1	2
Completeness [%]	98.1
Redundancy	5.1	5.1
CC(1/2)	0.998	0.774

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.