8DZB | pdb_00008dzb

Crystal structure of the SARS-CoV-2 (COVID-19) main protease in complex with inhibitor 11

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7RN1

Crystallization

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

Crystal Properties
Matthews coefficient	Solvent content
2.01	38.78

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 45.78	α = 90
b = 52.55	β = 100.23
c = 113.537	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 EIGER X 16M		2021-03-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	1	APS	22-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	1.85	47.6	94.7	0.087	0.101	0.049	0.994	9.8	3.7		21495

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	1.85	1.89	97.2		0.443	0.52	0.266	0.589		3.7

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	7RN1	1.85	47.6	20416	1078	94.23	0.1846	0.1833	0.19	0.2096	0.21	RANDOM	19.833

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]
-0.43		0.31	-0.22		0.51

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.439
r_dihedral_angle_4_deg	21.038
r_dihedral_angle_3_deg	14.651
r_dihedral_angle_1_deg	7.489
r_angle_refined_deg	1.66
r_angle_other_deg	1.401
r_chiral_restr	0.084
r_bond_refined_d	0.011
r_gen_planes_refined	0.009
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.439
r_dihedral_angle_4_deg	21.038
r_dihedral_angle_3_deg	14.651
r_dihedral_angle_1_deg	7.489
r_angle_refined_deg	1.66
r_angle_other_deg	1.401
r_chiral_restr	0.084
r_bond_refined_d	0.011
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2340
Nucleic Acid Atoms
Solvent Atoms	84
Heterogen Atoms	47

Software

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

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.