31GJ

Crystal structure of SARS-CoV-2 main protease (MPro) inactive mutant C145A in complex with Nirmatrelvir

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	2025-09-16
Detector	DECTRIS EIGER X 16M
Wavelength(s)	0.9762
Spacegroup name	P 21 21 21
Unit cell lengths	67.929, 101.249, 104.037
Unit cell angles	90.00, 90.00, 90.00

Refinement procedure

Resolution	56.880 - 1.820
R-factor	0.1956
Rwork	0.194
R-free	0.23330
Structure solution method	FOURIER SYNTHESIS
RMSD bond length	0.005
RMSD bond angle	0.808
Data scaling software	Aimless (0.8.2)
Phasing software	PHENIX ((2.1_6048: ???))
Refinement software	PHENIX ((2.1_6048: ???))

Data quality characteristics

	Overall	Outer shell
Low resolution limit [Å]	72.560	2.010
High resolution limit [Å]	1.820	1.820
Rmerge	0.211	2.705
Rmeas	0.220	2.803
Rpim	0.059	0.731
Number of reflections	45798	2290
<I/σ(I)>	8.2	1.5
Completeness [%]	94.6	70.1
Redundancy	13.8	14.6
CC(1/2)	0.998	0.605

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, HANGING DROP	7.7	293	0.1 M MIB pH 7.7, 23.5% PEG 1500, 5% DMSO, 1 mM DTT, 0.25 mM EDTA