7K40

Crystal Structure of SARS-CoV-2 Main Protease (3CLpro/Mpro) in Complex with Covalent Inhibitor Boceprevir at 1.35 A Resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6WNPPDB entry 6WNP

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.229820% PEG4000, 0.1 M HEPES, pH 7.2, 0.1 M sodium chloride, 4% DMSO
Crystal Properties
Matthews coefficientSolvent content
2.0239.15

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 114.279α = 90
b = 53.321β = 101.7
c = 45.835γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2020-09-08MSINGLE 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
11.3527.9999.20.0450.0490.020.99916.45.659261
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)
11.351.3889.91.2431.3960.6190.5054.7

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 REPLACEMENTTHROUGHOUTPDB entry 6WNP1.3527.9856241300599.160.17090.16980.1915RANDOM24.194
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]
-0.010.32-0.220.09
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.268
r_dihedral_angle_4_deg11.399
r_dihedral_angle_3_deg10.792
r_dihedral_angle_1_deg7.034
r_angle_refined_deg1.989
r_angle_other_deg1.747
r_chiral_restr0.121
r_bond_refined_d0.015
r_gen_planes_refined0.012
r_gen_planes_other0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.268
r_dihedral_angle_4_deg11.399
r_dihedral_angle_3_deg10.792
r_dihedral_angle_1_deg7.034
r_angle_refined_deg1.989
r_angle_other_deg1.747
r_chiral_restr0.121
r_bond_refined_d0.015
r_gen_planes_refined0.012
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2367
Nucleic Acid Atoms
Solvent Atoms295
Heterogen Atoms57

Software

Software
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
PHASERphasing