8INX

Crystal Structure of SARS-CoV-2 Main Protease (Mpro) G15S Mutant in Complex with Inhibitor ensitrelvir


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 8HBK 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1EVAPORATION2934% v/v TacsimateTM pH 4.0, 12% w/v Polyethylene glycol 3,350
Crystal Properties
Matthews coefficientSolvent content
2.856.15

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 97.75α = 90
b = 83.137β = 115.14
c = 51.632γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 X 16M2023-03-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.953740DiamondI04

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim 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
11.6629.6899.50.0409999999999999950.045119.486.943904
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.661.760.88099999999999990.950.897

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTNONE1.6629.681.3643846199999.670.1980.19690.2205
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]
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d7.958
f_angle_d0.939
f_chiral_restr0.055
f_plane_restr0.007
f_bond_d0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2331
Nucleic Acid Atoms
Solvent Atoms219
Heterogen Atoms37

Software

Software
Software NamePurpose
XSCALEdata scaling
PHENIXrefinement
autoPROCdata reduction
PHENIXphasing