9G0H

Crystal structure of SARS-CoV-2 main protease (MPro) in complex with the noncovalently bound inhibitor C5N17A

This is a non-PDB format compatible entry.

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)
Synchrotron site	PETRA III, EMBL c/o DESY
Beamline	P13 (MX1)
Temperature [K]	100
Detector technology	PIXEL
Collection date	2023-12-16
Detector	DECTRIS EIGER X 16M
Wavelength(s)	0.9762
Spacegroup name	P 21 21 21
Unit cell lengths	67.887, 99.889, 104.104
Unit cell angles	90.00, 90.00, 90.00

Refinement procedure

Resolution	46.160 - 1.650
R-factor	0.1869
Rwork	0.185
R-free	0.22170
Structure solution method	FOURIER SYNTHESIS
RMSD bond length	0.005
RMSD bond angle	0.759
Data reduction software	XDS (Jun 30, 2023 (BUILT 20230630))
Data scaling software	Aimless (0.7.7)
Phasing software	PHENIX
Refinement software	PHENIX ((1.18.2_3874: ???))

Data quality characteristics

	Overall	Outer shell
Low resolution limit [Å]	72.080	1.840
High resolution limit [Å]	1.650	1.650
Rmerge	0.089	1.648
Rmeas	0.092
Rpim	0.025	0.466
Number of reflections	55044	2752
<I/σ(I)>	17.5	1.7
Completeness [%]	95.4	72.1
Redundancy	13.5	13.4
CC(1/2)	0.999	0.659

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION		295	1.5 mM inhibitor, 24% PEG1500, 0.05 M sodium malonate, 0.075 M imidazole, 0.075 M boric acid, 5 % DMSO, 1 mM DTT, 1.58 mM EDTA, 26.67 mM Tris, 20 mM NaCl, 1.33 mM TCEP, pH 7.8