9ARQ

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


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP29828% v/v 2-Propanol, 0.1 M BIS-TRIS pH 6.5, 3% v/v Polyethylene glycol 200
Crystal Properties
Matthews coefficientSolvent content
2.2846.05

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 45.627α = 90
b = 63.997β = 90
c = 105.646γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 4M2024-02-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS-II BEAMLINE 19-ID0.979497NSLS-II19-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
1241.9294.30.1149.33.820285
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.0022.05463.40.782.3

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 REPLACEMENTTHROUGHOUT241.9219266101994.130.1840.181260.2355RANDOM29.211
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]
-0.151.01-0.86
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg16.041
r_dihedral_angle_3_deg13.659
r_dihedral_angle_1_deg7.254
r_long_range_B_refined7.006
r_long_range_B_other7.005
r_scangle_other5.322
r_scbond_it3.487
r_scbond_other3.482
r_mcangle_it3.475
r_mcangle_other3.475
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg16.041
r_dihedral_angle_3_deg13.659
r_dihedral_angle_1_deg7.254
r_long_range_B_refined7.006
r_long_range_B_other7.005
r_scangle_other5.322
r_scbond_it3.487
r_scbond_other3.482
r_mcangle_it3.475
r_mcangle_other3.475
r_mcbond_it2.408
r_mcbond_other2.407
r_angle_refined_deg1.891
r_angle_other_deg0.79
r_chiral_restr0.09
r_bond_refined_d0.01
r_gen_planes_refined0.01
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 Atoms91
Heterogen Atoms45

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
DIALSdata scaling
MOLREPphasing