Experiment: 8V4U

Structure of SARS-CoV-2 main protease in complex with a covalent inhibitor

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		294	20.0% w/v PEG 3350 and 0.2 M potassium sodium tartrate tetrahydrate

Crystal Properties
Matthews coefficient	Solvent content
2.05	39.93

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 45.407	α = 90
b = 54.138	β = 101.86
c = 115.15	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	98	PIXEL	DECTRIS EIGER X 9M		2021-11-09	M	SINGLE WAVELENGTH

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

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.82	112.69	92.4	0.089	0.057	0.998	8.3	3.5		33628

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.82	2	53.4		0.759	0.485	0.618	1.5	3.4

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	FOURIER SYNTHESIS	THROUGHOUT	1.819	112.69	33628	1665	68.1	0.2186	0.2161	0.2091	0.264	0.2547	RANDOM	31.34

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]
0.0971		0.4282	-0.6952		0.5981

RMS Deviations
Key	Refinement Restraint Deviation
t_other_torsion	16.96
t_omega_torsion	3.63
t_angle_deg	0.99
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	4681
Nucleic Acid Atoms
Solvent Atoms	247
Heterogen Atoms	68

Software

Software
Software Name	Purpose
BUSTER	refinement
autoPROC	data reduction
STARANISO	data scaling
DIMPLE	phasing