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A novel, covalent and highly synthetically accessible SARS-CoV-2 Mpro chloroacetamide inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6W63
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.9 291 0.2 M LiSO4, pH 7.9, 12% PEG3350
Crystal Properties Matthews coefficient Solvent content 2.25 45.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.83 α = 90 b = 63.37 β = 90 c = 106.81 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS3 6M 2020-09-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID09 1.18064 ESRF ID09
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.82 48.83 99.8 0.084 13.8 7.5 46287
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.82 1.86 0.084
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 6W63 1.82 40.87 26448 1375 99.08 0.23216 0.22998 0.2401 0.2761 0.2878 RANDOM 22.759
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] 0.27 1.22 -1.49
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.914 r_dihedral_angle_3_deg 13.273 r_dihedral_angle_4_deg 12.752 r_dihedral_angle_1_deg 6.977 r_long_range_B_refined 4.039 r_long_range_B_other 3.717 r_mcangle_it 1.472 r_mcangle_other 1.471 r_angle_refined_deg 1.209 r_scangle_other 1.159
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.914 r_dihedral_angle_3_deg 13.273 r_dihedral_angle_4_deg 12.752 r_dihedral_angle_1_deg 6.977 r_long_range_B_refined 4.039 r_long_range_B_other 3.717 r_mcangle_it 1.472 r_mcangle_other 1.471 r_angle_refined_deg 1.209 r_scangle_other 1.159 r_angle_other_deg 1.124 r_mcbond_other 0.805 r_mcbond_it 0.804 r_scbond_it 0.641 r_scbond_other 0.641 r_chiral_restr 0.047 r_gen_planes_refined 0.003 r_bond_refined_d 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 Atoms Number Protein Atoms 2358 Nucleic Acid Atoms Solvent Atoms 304 Heterogen Atoms 89
Software Software Software Name Purpose REFMAC refinement