8HEF

The Crystal structure of deuterated S-217622 (Ensitrelvir) bound to the main protease (3CLpro/Mpro) of SARS-CoV-2


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7BE7 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP82890.2 M Ammonium acetate, 15% (w/v) PEG3350
Crystal Properties
Matthews coefficientSolvent content
2.3447.54

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 55.8α = 90
b = 99.06β = 108.8
c = 59.67γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2022-08-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL19U10.97849SSRFBL19U1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)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
11.5137.2799.80.0710.077210.030240.99914.76.39586415.23
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.511.5598.290.86170.97230.43990.6711.64.6

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 REPLACEMENTTHROUGHOUT7BE71.5137.2791036479699.760.134550.132650.17009RANDOM21.023
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]
0.76-1.470.24
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.375
r_dihedral_angle_4_deg18.524
r_dihedral_angle_3_deg11.632
r_dihedral_angle_1_deg6.289
r_long_range_B_refined3.404
r_long_range_B_other3.22
r_scangle_other2.563
r_mcangle_it2.302
r_mcangle_other2.302
r_rigid_bond_restr2.199
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.375
r_dihedral_angle_4_deg18.524
r_dihedral_angle_3_deg11.632
r_dihedral_angle_1_deg6.289
r_long_range_B_refined3.404
r_long_range_B_other3.22
r_scangle_other2.563
r_mcangle_it2.302
r_mcangle_other2.302
r_rigid_bond_restr2.199
r_scbond_it1.989
r_scbond_other1.988
r_mcbond_it1.721
r_mcbond_other1.712
r_angle_refined_deg1.577
r_angle_other_deg1.209
r_chiral_restr0.108
r_bond_refined_d0.013
r_gen_planes_refined0.009
r_bond_other_d0.001
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_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4643
Nucleic Acid Atoms
Solvent Atoms521
Heterogen Atoms80

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
PHASERphasing