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SARS-CoV-2 3CLpro bound to covalent inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6LU7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 293 0.2M sodium fluoride, 20% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2 38.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.54 α = 90 b = 52.94 β = 100.72 c = 113.96 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 PILATUS 6M 2022-06-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID09 0.987 ESRF ID09
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.45 47.91 99.9 0.151 0.997 8.6 6.8 19865
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.45 2.55 0.047 0.999
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 2.45 47.91 18877 981 99.78 0.25377 0.25136 0.2574 0.29942 0.3009 RANDOM 38.095
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] -1.03 -1.9 -1.1 2.66
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.445 r_dihedral_angle_3_deg 14.537 r_dihedral_angle_4_deg 11.462 r_dihedral_angle_1_deg 7.136 r_long_range_B_refined 4.36 r_long_range_B_other 4.36 r_mcangle_it 2.586 r_mcangle_other 2.586 r_scangle_other 2.084 r_mcbond_it 1.507
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.445 r_dihedral_angle_3_deg 14.537 r_dihedral_angle_4_deg 11.462 r_dihedral_angle_1_deg 7.136 r_long_range_B_refined 4.36 r_long_range_B_other 4.36 r_mcangle_it 2.586 r_mcangle_other 2.586 r_scangle_other 2.084 r_mcbond_it 1.507 r_mcbond_other 1.507 r_angle_refined_deg 1.266 r_scbond_it 1.203 r_scbond_other 1.203 r_angle_other_deg 1.088 r_chiral_restr 0.041 r_bond_refined_d 0.003 r_gen_planes_refined 0.003 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 4716 Nucleic Acid Atoms Solvent Atoms 16 Heterogen Atoms 70
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing