8DOY

Crystal structure of SARS-CoV-2 main protease in complex with an inhibitor TKB-198


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 6.0, 15% polyethyene glycol (PEG) 6000 and 3% DMSO
Crystal Properties
Matthews coefficientSolvent content
2.1943.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.046α = 90
b = 98.942β = 106.28
c = 57.724γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2021-08-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL41XU1SPring-8BL41XU

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rrim 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
11.5998.9491.040.22215.598.376634
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)
11.5911.6480.762

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 7JKV1.5955.4772879373298.270.199550.197250.24566RANDOM30.965
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]
-1.14-1.380.441.28
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg14.624
r_dihedral_angle_2_deg12.039
r_dihedral_angle_1_deg7.809
r_long_range_B_refined7.226
r_long_range_B_other7.225
r_scangle_other4.936
r_mcangle_it3.936
r_mcangle_other3.935
r_scbond_it3.418
r_scbond_other3.417
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg14.624
r_dihedral_angle_2_deg12.039
r_dihedral_angle_1_deg7.809
r_long_range_B_refined7.226
r_long_range_B_other7.225
r_scangle_other4.936
r_mcangle_it3.936
r_mcangle_other3.935
r_scbond_it3.418
r_scbond_other3.417
r_mcbond_it2.584
r_mcbond_other2.583
r_angle_refined_deg1.561
r_angle_other_deg0.573
r_chiral_restr0.072
r_bond_refined_d0.009
r_gen_planes_refined0.009
r_bond_other_d0.001
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 Atoms4666
Nucleic Acid Atoms
Solvent Atoms142
Heterogen Atoms130

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata reduction
MOLREPphasing
Cootmodel building
xia2data scaling