8VDJ | pdb_00008vdj

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

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6LU7

Crystallization

Crystalization Experiments
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.

Crystal Properties
Matthews coefficient	Solvent content
2.49	50.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 67.451	α = 90
b = 99.13	β = 90
c = 100.626	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS EIGER2 X 9M		2022-07-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 17-ID	1.000	APS	17-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2.002	70.618	85.8	0.1259	0.1371	0.0537	0.998	9.73	6.49		25441

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.002	2.219	63.3		0.8326	0.9085	0.3588	0.595	2.17	6.22	1272

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.002	31.77	25433	1199	55.1	0.2369	0.2352	0.2312	0.2707	0.2669	RANDOM	40.35

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
-4.1316			12.6158		-8.4842

RMS Deviations
Key	Refinement Restraint Deviation
t_other_torsion	14.97
t_omega_torsion	3.68
t_angle_deg	0.65
t_bond_d	0.008
t_dihedral_angle_d
t_gen_planes
t_it
t_chiral_improper_torsion
t_ideal_dist_contact

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4624
Nucleic Acid Atoms
Solvent Atoms	152
Heterogen Atoms	81

Software

Software
Software Name	Purpose
BUSTER	refinement
XDS	data reduction
Aimless	data scaling
autoPROC	data processing
PHASER	phasing