9QD5

Crystal structure of SARS-CoV-2 main protease in complex with RS222C

This is a non-PDB format compatible entry.

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	DIAMOND BEAMLINE I03
Synchrotron site	Diamond
Beamline	I03
Temperature [K]	100
Detector technology	PIXEL
Collection date	2023-07-16
Detector	DECTRIS EIGER2 XE 16M
Wavelength(s)	0.97625
Spacegroup name	P 21 21 21
Unit cell lengths	67.742, 99.931, 104.108
Unit cell angles	90.00, 90.00, 90.00

Refinement procedure

Resolution	72.093 - 2.044
Rwork	0.190
R-free	0.23190
Structure solution method	MOLECULAR REPLACEMENT
RMSD bond length	0.010
RMSD bond angle	1.377
Data reduction software	XDS (Jan 10, 2022)
Data scaling software	Aimless (0.7.9)
Refinement software	REFMAC (5.8.0425)

Data quality characteristics

	Overall	Inner shell	Outer shell
Low resolution limit [Å]	72.093	72.093	2.230
High resolution limit [Å]	2.044	6.500	2.044
Rmerge	0.199	0.057	1.823
Rmeas	0.207	0.060	1.892
Rpim	0.056	0.018	0.502
Total number of observations	412470	19869	20848
Number of reflections	31215	1561	1561
<I/σ(I)>	9.71	27.37	1.61
Completeness [%]	93.2	99.9	60.4
Completeness (spherical) [%]	68.7	99.9	15.2
Completeness (ellipsoidal) [%]	93.2	99.9	60.4
Redundancy	13.21	12.73	13.36
CC(1/2)	0.918	0.740	0.665
Anomalous completeness (spherical)	68.1	100.0	14.8
Anomalous completeness	93.5	100.0	60.7
Anomalous redundancy	7.0	7.7	7.0
CC(ano)	-0.052	-0.215	0.008
|DANO|/σ(DANO)	0.7	0.6	0.7

Diffraction limits	Principal axes of ellipsoid fitted to diffraction cut-off surface
2.114 Å	1.000, 1.000, 1.000
2.701 Å	0.000, 0.000, 0.000
2.043 Å	0.000, 0.000, 0.000
Criteria used in determination of diffraction limits	local <I/sigmaI> ≥ 1.2

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP	6.7	293	100 mM MES pH 6.7, 11% PEG 4000 and 5% DMSO 150 nL Protein (5 mg/mL), 150 nL Crystallisation condition, 50 nL seed stock (1:250)