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)
TypeSourceAccession CodeDetails
experimental modelPDB 6YB7 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.529820% PEG 3350, 0.1 M MES pH 6.5, 5% DMSO
Crystal Properties
Matthews coefficientSolvent content
1.9235.92

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 44.784α = 90
b = 52.931β = 100.07
c = 111.273γ = 90
Symmetry
Space GroupI 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2020-06-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS-II BEAMLINE 17-ID-20.9793NSLS-II17-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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.227.3997.80.0940.1030.0420.99711.66.278254
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)RedundancyNumber Unique Reflections (All)
11.21.2264.50.8690.9740.4280.6734.4

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT6YB71.227.3974325390097.70.13670.13510.1674RANDOM16.705
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]
-0.26-0.020.220.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.193
r_dihedral_angle_3_deg12.015
r_dihedral_angle_4_deg10.102
r_dihedral_angle_1_deg6.944
r_rigid_bond_restr6.719
r_angle_refined_deg2.206
r_angle_other_deg1.694
r_chiral_restr0.135
r_bond_refined_d0.022
r_gen_planes_refined0.013
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.193
r_dihedral_angle_3_deg12.015
r_dihedral_angle_4_deg10.102
r_dihedral_angle_1_deg6.944
r_rigid_bond_restr6.719
r_angle_refined_deg2.206
r_angle_other_deg1.694
r_chiral_restr0.135
r_bond_refined_d0.022
r_gen_planes_refined0.013
r_gen_planes_other0.01
r_bond_other_d0.009
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2367
Nucleic Acid Atoms
Solvent Atoms339
Heterogen Atoms46

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PDB_EXTRACTdata extraction
PHASERphasing