9ARS

Crystal structure of SARS-CoV-2 main protease E166V mutant in complex with an inhibitor TKB-245


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 8UH9 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2980.1 M HEPES pH 7.5, 14 % w/v Polyethylene glycol 3,350
Crystal Properties
Matthews coefficientSolvent content
2.0740.66

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 45.931α = 90
b = 53.951β = 100.38
c = 114.966γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 4M2023-09-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS-II BEAMLINE 19-ID0.979497NSLS-II19-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
12.445.1898.660.0656214.263.821740
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.42.510.5237

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT2.448.6920612112698.850.179910.177560.22195RANDOM50.338
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]
-1.56-0.311.330.32
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg14.904
r_long_range_B_refined9.425
r_long_range_B_other9.425
r_dihedral_angle_1_deg7.859
r_dihedral_angle_2_deg7.375
r_scangle_other7.091
r_mcangle_it5.978
r_mcangle_other5.977
r_scbond_it4.674
r_scbond_other4.674
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg14.904
r_long_range_B_refined9.425
r_long_range_B_other9.425
r_dihedral_angle_1_deg7.859
r_dihedral_angle_2_deg7.375
r_scangle_other7.091
r_mcangle_it5.978
r_mcangle_other5.977
r_scbond_it4.674
r_scbond_other4.674
r_mcbond_it3.973
r_mcbond_other3.972
r_angle_refined_deg1.69
r_angle_other_deg0.684
r_chiral_restr0.076
r_bond_refined_d0.008
r_gen_planes_refined0.007
r_bond_other_d0.002
r_gen_planes_other0.001
r_dihedral_angle_4_deg
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4730
Nucleic Acid Atoms
Solvent Atoms29
Heterogen Atoms90

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
DIALSdata scaling
MOLREPphasing