8P5B

Crystal structure of the main protease (3CLpro/Mpro) of SARS-CoV-2 obtained in presence of 500 micromolar X77 enantiomer S.


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2930.1 M Sodium formate 0.1M Ammonium acetate 0.1M Sodium citrate tribasic dihydrate 0.1M Potassium sodium tartrate tetrahydrate 0.1M Sodium oxamate, 0.1M imidazole/MES pH 6.5, 12.5% v/v MPD 12.5% PEG 1000 12.5% w/v PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.652.68

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 67.93α = 90
b = 99.831β = 90
c = 103.72γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2021-06-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONELETTRA BEAMLINE 11.2C0.9718ELETTRA11.2C

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.47103.721000.0760.99913.98.912155118.33
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.471.490.664

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 REPLACEMENTFREE R-VALUE7BB21.4751.861.33121365599399.880.16510.16440.17827.39
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_d13.7404
f_angle_d0.9332
f_chiral_restr0.0749
f_plane_restr0.0076
f_bond_d0.0063
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4726
Nucleic Acid Atoms
Solvent Atoms677
Heterogen Atoms18

Software

Software
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing