8HOM

Crystal Structure of SARS-CoV-2 Omicron Main Protease (Mpro) in Complex with Ensitrelvir


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7VH8 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1EVAPORATION2930.1 M Tris pH 7.6, 14% v/v ethylene glycol, 7% w/v PEG 8000
Crystal Properties
Matthews coefficientSolvent content
2.7455.03

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 97.02α = 90
b = 81.493β = 114.61
c = 51.545γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2022-08-20MSINGLE 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
11.5629.2599.50.0380.042121.686.952134
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)
11.561.650.5730.6170.9279999999999999

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 REPLACEMENTNONE1.5629.251.3552108199599.660.17110.17010.1961
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_d8.107
f_angle_d0.917
f_chiral_restr0.052
f_plane_restr0.009
f_bond_d0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2317
Nucleic Acid Atoms
Solvent Atoms167
Heterogen Atoms37

Software

Software
Software NamePurpose
XSCALEdata scaling
PHENIXrefinement
AutoProcessdata reduction
PHENIXphasing