8DOX

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


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7JKVPDB entry 7JKV

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2980.1 M MES, pH 5.8, 15% PEG6000, 3% DMSO
Crystal Properties
Matthews coefficientSolvent content
1.9938.34

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 115.333α = 90
b = 52.913β = 103.74
c = 45.604γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2021-07-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL24XU1SPring-8BL24XU

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
11.4656.0299.10.1788.688.546005
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)
11.461.499.082

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 REPLACEMENTTHROUGHOUTPDB entry 7JKV1.4656.0243680232299.040.200880.199350.22893RANDOM26.529
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]
0.910.04-0.09-0.75
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.979
r_dihedral_angle_4_deg18.802
r_dihedral_angle_3_deg13.689
r_dihedral_angle_1_deg7.283
r_long_range_B_refined5.924
r_long_range_B_other5.923
r_scangle_other4.459
r_mcangle_it3.026
r_mcangle_other3.025
r_scbond_it2.893
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.979
r_dihedral_angle_4_deg18.802
r_dihedral_angle_3_deg13.689
r_dihedral_angle_1_deg7.283
r_long_range_B_refined5.924
r_long_range_B_other5.923
r_scangle_other4.459
r_mcangle_it3.026
r_mcangle_other3.025
r_scbond_it2.893
r_scbond_other2.892
r_mcbond_it2.023
r_mcbond_other2.023
r_angle_refined_deg1.644
r_angle_other_deg1.408
r_chiral_restr0.077
r_bond_refined_d0.011
r_gen_planes_refined0.01
r_bond_other_d0.002
r_gen_planes_other0.001
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 Atoms2337
Nucleic Acid Atoms
Solvent Atoms119
Heterogen Atoms49

Software

Software
Software NamePurpose
REFMACrefinement
Cootmodel building
PDB_EXTRACTdata extraction
MOLREPphasing
xia2data reduction
DIALSdata scaling