7K3T

Crystal Structure of SARS-CoV-2 Main Protease (3CLpro/Mpro) at 1.2 A Resolution and a Possible Capture of Zinc Binding Intermediate

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6YB7

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	298	20% PEG 3350, 0.1 M MES pH 6.5, 5% DMSO

Crystal Properties
Matthews coefficient	Solvent content
1.92	35.92

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 44.784	α = 90
b = 52.931	β = 100.07
c = 111.273	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		2020-06-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS-II BEAMLINE 17-ID-2	0.9793	NSLS-II	17-ID-2

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	1.2	27.39	97.8	0.094	0.103	0.042	0.997	11.6	6.2		78254

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	1.2	1.22	64.5		0.869	0.974	0.428	0.673		4.4

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	6YB7	1.2	27.39	74325	3900	97.7	0.1367	0.1351	0.1674	RANDOM	16.705

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]
-0.26		-0.02	0.22		0.04

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.193
r_dihedral_angle_3_deg	12.015
r_dihedral_angle_4_deg	10.102
r_dihedral_angle_1_deg	6.944
r_rigid_bond_restr	6.719
r_angle_refined_deg	2.206
r_angle_other_deg	1.694
r_chiral_restr	0.135
r_bond_refined_d	0.022
r_gen_planes_refined	0.013

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.193
r_dihedral_angle_3_deg	12.015
r_dihedral_angle_4_deg	10.102
r_dihedral_angle_1_deg	6.944
r_rigid_bond_restr	6.719
r_angle_refined_deg	2.206
r_angle_other_deg	1.694
r_chiral_restr	0.135
r_bond_refined_d	0.022
r_gen_planes_refined	0.013
r_gen_planes_other	0.01
r_bond_other_d	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2367
Nucleic Acid Atoms
Solvent Atoms	339
Heterogen Atoms	46

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PDB_EXTRACT	data extraction
PHASER	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.