8UH9

Crystal structure of SARS-CoV-2 main protease E166V mutant in complex with an inhibitor TKB-272


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2980.4 M Sodium acetate trihydrate, pH 5.8, 30% PEG 400, 3% DMSO
Crystal Properties
Matthews coefficientSolvent content
1.9938.04

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 113.673α = 90
b = 53.09β = 101.96
c = 45.774γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2022-07-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL41XU1.0SPring-8BL41XU

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rpim I (All)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
12.06755.699.50.1085.986.916462
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)
12.0672.10.280.26

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 REPLACEMENTTHROUGHOUT2.06755.61583562699.740.194130.191910.24028RANDOM59.194
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]
1.570.230.49-1.98
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg17.483
r_dihedral_angle_2_deg12.894
r_long_range_B_refined10.394
r_long_range_B_other10.392
r_dihedral_angle_1_deg8.16
r_scangle_other7.583
r_mcangle_it6.229
r_mcangle_other6.227
r_scbond_it4.869
r_scbond_other4.867
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg17.483
r_dihedral_angle_2_deg12.894
r_long_range_B_refined10.394
r_long_range_B_other10.392
r_dihedral_angle_1_deg8.16
r_scangle_other7.583
r_mcangle_it6.229
r_mcangle_other6.227
r_scbond_it4.869
r_scbond_other4.867
r_mcbond_it4.205
r_mcbond_other4.204
r_angle_refined_deg1.47
r_angle_other_deg0.586
r_chiral_restr0.057
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 Atoms2365
Nucleic Acid Atoms
Solvent Atoms4
Heterogen Atoms52

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata reduction
DIALSdata scaling
MOLREPphasing