7MNG

Crystal Structure of SARS-CoV-2 Main Protease (3CLpro/Mpro) in Complex with Covalent Inhibitor VBY-825 (Partial Occupancy)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7K40 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7293PEG 4000, HEPES pH 7.0, 1 mM VBY-825 (in final drop), 4% DMSO (in final drop)
Crystal Properties
Matthews coefficientSolvent content
2.0239.25

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 114.706α = 90
b = 53.896β = 101.1
c = 44.75γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2021-03-21MSINGLE 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
11.728.141000.1840.1940.0590.997910.329633
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)
11.71.731002.4882.6270.8340.6089.5

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 REPLACEMENTTHROUGHOUT7K401.728.1628079148299.730.18140.17950.2179RANDOM26.133
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]
-0.010.010.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.77
r_dihedral_angle_4_deg19.098
r_dihedral_angle_3_deg14.227
r_dihedral_angle_1_deg7.39
r_angle_other_deg3.974
r_angle_refined_deg1.701
r_bond_other_d1.589
r_chiral_restr0.145
r_gen_planes_other0.022
r_bond_refined_d0.012
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.77
r_dihedral_angle_4_deg19.098
r_dihedral_angle_3_deg14.227
r_dihedral_angle_1_deg7.39
r_angle_other_deg3.974
r_angle_refined_deg1.701
r_bond_other_d1.589
r_chiral_restr0.145
r_gen_planes_other0.022
r_bond_refined_d0.012
r_gen_planes_refined0.012
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2367
Nucleic Acid Atoms
Solvent Atoms305
Heterogen Atoms104

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PDB_EXTRACTdata extraction
PHASERphasing