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The Crystal structure of mol066 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 2.31 46.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.475 α = 90 b = 99.384 β = 108.15 c = 58.793 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 1.8 55.93 97.85 0.999 18.49 2 54881 21.4
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 1.8 1.864 0.958
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.8 55.93 52185 2696 97.87 0.14995 0.14813 0.1573 0.18587 0.1938 RANDOM 21.619
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] -0.21 -1.44 -0.06 1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.927 r_dihedral_angle_1_deg 6.506 r_long_range_B_refined 6.466 r_long_range_B_other 6.305 r_scangle_other 5.345 r_scbond_it 3.683 r_scbond_other 3.683 r_dihedral_angle_2_deg 3.574 r_mcangle_it 3.512 r_mcangle_other 3.512
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.927 r_dihedral_angle_1_deg 6.506 r_long_range_B_refined 6.466 r_long_range_B_other 6.305 r_scangle_other 5.345 r_scbond_it 3.683 r_scbond_other 3.683 r_dihedral_angle_2_deg 3.574 r_mcangle_it 3.512 r_mcangle_other 3.512 r_mcbond_it 2.568 r_mcbond_other 2.566 r_angle_refined_deg 1.39 r_angle_other_deg 0.501 r_chiral_restr 0.069 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.002 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 4736 Nucleic Acid Atoms Solvent Atoms 490 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement Coot model building autoPROC data reduction autoPROC data scaling PHASER phasing