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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, HANGING DROP 291 0.1 M Sodium acetate pH 4.6, 8 % w/v PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.74 55.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.46 α = 90 b = 80.98 β = 115.69 c = 51.34 γ = 90
Symmetry Space Group C 1 2 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 2022-06-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID09 0.96546 ESRF ID09
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 1.56 46.31 97.4 0.996 12.9 6.8 50168
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 1.56 1.59 0.818
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 1.56 46.31 47381 2518 96.69 0.18055 0.17915 0.1917 0.20713 0.2187 RANDOM 27.637
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] 0.7 -0.33 1.91 -1.56
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.306 r_dihedral_angle_4_deg 18.566 r_dihedral_angle_3_deg 13.722 r_long_range_B_refined 7.755 r_long_range_B_other 7.732 r_dihedral_angle_1_deg 7.189 r_scangle_other 5.694 r_mcangle_it 3.964 r_mcangle_other 3.964 r_scbond_it 3.762
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.306 r_dihedral_angle_4_deg 18.566 r_dihedral_angle_3_deg 13.722 r_long_range_B_refined 7.755 r_long_range_B_other 7.732 r_dihedral_angle_1_deg 7.189 r_scangle_other 5.694 r_mcangle_it 3.964 r_mcangle_other 3.964 r_scbond_it 3.762 r_scbond_other 3.761 r_mcbond_it 2.79 r_mcbond_other 2.779 r_angle_refined_deg 1.866 r_angle_other_deg 1.502 r_chiral_restr 0.099 r_bond_refined_d 0.013 r_gen_planes_refined 0.012 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 251 Heterogen Atoms 45
Software Software Software Name Purpose REFMAC refinement XDS data scaling XDS data reduction MOLREP phasing