8VDJ

Crystal structure of SARS-CoV-2 3CL protease (3CLpro) as a covalent complex with EDP-235

This is a non-PDB format compatible entry.

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	APS BEAMLINE 17-ID
Synchrotron site	APS
Beamline	17-ID
Temperature [K]	100
Detector technology	PIXEL
Collection date	2022-07-10
Detector	DECTRIS EIGER2 X 9M
Wavelength(s)	1.000
Spacegroup name	P 21 21 21
Unit cell lengths	67.451, 99.130, 100.626
Unit cell angles	90.00, 90.00, 90.00

Refinement procedure

Resolution	31.770 - 2.002
R-factor	0.2369
Rwork	0.235
R-free	0.27070
Structure solution method	MOLECULAR REPLACEMENT
RMSD bond length	0.008
RMSD bond angle	0.650
Data reduction software	XDS (Feb 5, 2021 (BUILT 20210323))
Data scaling software	Aimless (0.7.7)
Phasing software	PHASER
Refinement software	BUSTER (2.11.8 (8-JUN-2022))

Data quality characteristics

	Overall	Inner shell	Outer shell
Low resolution limit [Å]	70.618	70.618	2.219
High resolution limit [Å]	2.002	6.863	2.002
Rmerge	0.126	0.044	0.833
Rmeas	0.137	0.048	0.908
Rpim	0.054	0.019	0.359
Total number of observations	165074	8175	7910
Number of reflections	25441	1272	1272
<I/σ(I)>	9.73	25.39	2.17
Completeness [%]	85.8	99.4	63.3
Completeness (spherical) [%]	55.1	99.4	10.6
Completeness (ellipsoidal) [%]	85.8	99.4	63.3
Redundancy	6.49	6.43	6.22
CC(1/2)	0.998	0.999	0.595
Anomalous completeness (spherical)	53.8	99.8	10.1
Anomalous completeness	85.0	99.8	62.9
Anomalous redundancy	3.5	3.8	3.3
CC(ano)	-0.203	-0.426	0.001
|DANO|/σ(DANO)	0.7	0.5	0.8

Diffraction limits	Principal axes of ellipsoid fitted to diffraction cut-off surface
1.920 Å	1.000, 1.000, 1.000
2.832 Å	0.000, 0.000, 0.000
2.309 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	7.5	293	The protein solution was incubated with DTT (0.22 mM) for 10 min on ice. Compound EDP-235 in DMSO (2.88 mM) was then added and incubated for 3 hrs on ice, then for 20 min at 18 C. Crystals appeared in drop with reservoir conditions: 0.2 M sodium thiocyanate, 20 % w/v PEG3350. The sample was harvested after 10 days growth and transferred to drop of neat reservoir condition. Cryoprotection was achieved by supplementing this drop with additional PEG400 to a final concentration of 5 % w/v PEG400 in reservoir condition. The sample was cryocooled by plunging into liquid nitrogen.