7RN0 | pdb_00007rn0

Crystal structure of the SARS-CoV-2 (COVID-19) main protease in complex with inhibitor Jun9-57-3R

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7KX5

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	25 % 3350, 0.2 M AmSO4, 0.1 M HEPES 7.5

Crystal Properties
Matthews coefficient	Solvent content
1.97	37.56

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 45.42	α = 90
b = 53.43	β = 101.37
c = 112.031	γ = 90

Symmetry
Space Group	I 1 2 1

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 PILATUS3 6M		2021-02-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.97890	APS	19-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	2.25	50	92.4	0.071	0.087	0.05	0.994	7.6	2.7		11614

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)
1	2.25	2.32	95.4		0.709	0.865	0.488	0.643		2.8

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	7KX5	2.25	48.05	11011	597	91.85	0.2151	0.2138	0.22	0.241	0.24	RANDOM	53.388

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]
-2.54		0.71	-0.75		2.78

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.263
r_dihedral_angle_4_deg	19.9
r_dihedral_angle_3_deg	17.813
r_dihedral_angle_1_deg	7.904
r_angle_refined_deg	1.62
r_angle_other_deg	1.312
r_chiral_restr	0.065
r_bond_refined_d	0.011
r_gen_planes_refined	0.008
r_bond_other_d	0.003

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.263
r_dihedral_angle_4_deg	19.9
r_dihedral_angle_3_deg	17.813
r_dihedral_angle_1_deg	7.904
r_angle_refined_deg	1.62
r_angle_other_deg	1.312
r_chiral_restr	0.065
r_bond_refined_d	0.011
r_gen_planes_refined	0.008
r_bond_other_d	0.003
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2326
Nucleic Acid Atoms
Solvent Atoms	22
Heterogen Atoms	45

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
iMOSFLM	data reduction
MOLREP	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.