8UH5

Crystal structure of SARS-CoV-2 main protease 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 DROP2980.1 M MES, pH 5.8, 15% PEG6000, 3% DMSO
Crystal Properties
Matthews coefficientSolvent content
238.55

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 114.003α = 90
b = 53.078β = 102.17
c = 45.783γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2022-05-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL41XU1SPring-8BL41XU

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.7455.7299.850.998911.98.627421
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)
11.741.770.3184

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 REPLACEMENTTHROUGHOUT1.7455.7226028139399.820.196020.19390.23299RANDOM46.261
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]
1.46-0.170.24-1.49
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg15.856
r_dihedral_angle_2_deg12.048
r_long_range_B_refined10.809
r_long_range_B_other10.807
r_scangle_other8.989
r_dihedral_angle_1_deg7.773
r_scbond_it6.456
r_scbond_other6.454
r_mcangle_it6.214
r_mcangle_other6.212
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg15.856
r_dihedral_angle_2_deg12.048
r_long_range_B_refined10.809
r_long_range_B_other10.807
r_scangle_other8.989
r_dihedral_angle_1_deg7.773
r_scbond_it6.456
r_scbond_other6.454
r_mcangle_it6.214
r_mcangle_other6.212
r_mcbond_it4.936
r_mcbond_other4.934
r_angle_refined_deg2.144
r_angle_other_deg0.792
r_chiral_restr0.103
r_bond_refined_d0.013
r_gen_planes_refined0.012
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 Atoms2367
Nucleic Acid Atoms
Solvent Atoms25
Heterogen Atoms52

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata reduction
CrystalCleardata scaling
MOLREPphasing