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The Crystal structure of mol080 bound to the main protease (3CLpro/Mpro) of SARS-CoV-2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8HEF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 289 0.2 M Ammonium acetate, 15% (w/v) PEG3350
Crystal Properties Matthews coefficient Solvent content 2.29 46.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.449 α = 90 b = 99.411 β = 108.05 c = 58.542 γ = 90
Symmetry Space Group P 1 21 1
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 2023-05-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.979 SSRF BL19U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 2.1 52.78 97.04 0.999 27.24 2 34208
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.175 1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.1 52.78 32491 1717 97.07 0.15305 0.15091 0.19336 0.203 RANDOM 18.249
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] -0.45 -1.39 -0.07 1.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.125 r_dihedral_angle_2_deg 7.433 r_dihedral_angle_1_deg 6.884 r_long_range_B_refined 6.204 r_long_range_B_other 6.055 r_scangle_other 4.139 r_mcangle_it 2.796 r_mcangle_other 2.796 r_scbond_it 2.607 r_scbond_other 2.607
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.125 r_dihedral_angle_2_deg 7.433 r_dihedral_angle_1_deg 6.884 r_long_range_B_refined 6.204 r_long_range_B_other 6.055 r_scangle_other 4.139 r_mcangle_it 2.796 r_mcangle_other 2.796 r_scbond_it 2.607 r_scbond_other 2.607 r_mcbond_it 1.757 r_mcbond_other 1.757 r_angle_refined_deg 1.333 r_angle_other_deg 0.45 r_chiral_restr 0.064 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 Atoms Number Protein Atoms 4734 Nucleic Acid Atoms Solvent Atoms 505 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction Aimless data scaling PHASER phasing