9SDM

Crystal structure of SARS-CoV-2 main protease (MPro) in complex with the covalently bound inhibitor GUE-4303 (compound 12 in publication)

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 P14 (MX2)
Synchrotron site	PETRA III, EMBL c/o DESY
Beamline	P14 (MX2)
Temperature [K]	100
Detector technology	PIXEL
Collection date	2025-04-05
Detector	DECTRIS EIGER2 X CdTe 16M
Wavelength(s)	1.3000
Spacegroup name	P 21 21 21
Unit cell lengths	67.838, 101.727, 104.045
Unit cell angles	90.00, 90.00, 90.00

Refinement procedure

Resolution	36.370 - 1.550
R-factor	0.1895
Rwork	0.187
R-free	0.23110
Structure solution method	FOURIER SYNTHESIS
RMSD bond length	0.012
RMSD bond angle	1.101
Data reduction software	XDS (Jan 19, 2025 (BUILT 20250327))
Data scaling software	Aimless (0.7.4)
Refinement software	PHENIX ((1.21.2_5419: ???))

Data quality characteristics

	Overall	Outer shell
Low resolution limit [Å]	72.740	1.700
High resolution limit [Å]	1.550	1.550
Rmerge	0.061	0.803
Rmeas	0.064	0.880
Rpim	0.018	0.353
Number of reflections	66567	3329
<I/σ(I)>	19.8	1.8
Completeness [%]	92.1
Redundancy	11.6
CC(1/2)	0.999	0.686

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION	7.7	295	23.5% PEG1500, 0.1M MIB (sodium malonate, imidazole and boric acid) pH 7.7, 5% DMSO, 1mM DTT, 0.25 mM EDTA