8DPR

Crystal structure of SARS-CoV-2 main protease in complex with inhibitor TKB-248


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2980.1 M MES, pH 5.8, 15% PEG6000, 3% DMSO
Crystal Properties
Matthews coefficientSolvent content
2.0840.97

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 115.403α = 90
b = 53.926β = 101.63
c = 45.678γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2021-10-09MSINGLE 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
1256.5299.90.9979.168.618600
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)
122.040.672

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 7JKV256.521766593499.860.192520.18970.24722RANDOM42.805
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]
1.87-0.53-0.01-1.52
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg16.957
r_long_range_B_refined8.234
r_long_range_B_other8.233
r_dihedral_angle_1_deg8.109
r_dihedral_angle_2_deg7.639
r_scangle_other6.286
r_mcangle_it4.973
r_mcangle_other4.972
r_scbond_it4.384
r_scbond_other4.383
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg16.957
r_long_range_B_refined8.234
r_long_range_B_other8.233
r_dihedral_angle_1_deg8.109
r_dihedral_angle_2_deg7.639
r_scangle_other6.286
r_mcangle_it4.973
r_mcangle_other4.972
r_scbond_it4.384
r_scbond_other4.383
r_mcbond_it3.609
r_mcbond_other3.608
r_angle_refined_deg1.648
r_angle_other_deg0.624
r_chiral_restr0.069
r_bond_refined_d0.01
r_gen_planes_refined0.009
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 Atoms2337
Nucleic Acid Atoms
Solvent Atoms11
Heterogen Atoms50

Software

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