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Crystal structure of SARS-CoV-2 main protease E166V mutant in complex with leritrelvir
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7VH8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 289 0.1 M Ammonium citrate tribasic pH 6.0, 14% w/v Polyethylene glycol 3350
Crystal Properties Matthews coefficient Solvent content 2.07 40.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.837 α = 90 b = 106.317 β = 103.218 c = 54.145 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 2024-09-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.97923 SSRF BL19U1
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 1.56 53.16 99.7 0.076 0.997 12.2 5.2 76106
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 1.56 1.59 0.859 0.615 2.4
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.56 53.159 75840 3863 99.355 0.15 0.1475 0.1552 0.1974 0.2082 21.353
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] 2.516 -0.094 1.641 -3.704
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 19.799 r_lrange_it 16.758 r_lrange_other 15.702 r_dihedral_angle_6_deg 15.512 r_dihedral_angle_3_deg 13.928 r_scangle_it 10.414 r_scangle_other 10.412 r_mcangle_it 8.871 r_mcangle_other 8.87 r_scbond_it 7.151
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 19.799 r_lrange_it 16.758 r_lrange_other 15.702 r_dihedral_angle_6_deg 15.512 r_dihedral_angle_3_deg 13.928 r_scangle_it 10.414 r_scangle_other 10.412 r_mcangle_it 8.871 r_mcangle_other 8.87 r_scbond_it 7.151 r_scbond_other 7.149 r_dihedral_angle_1_deg 6.913 r_mcbond_it 5.956 r_mcbond_other 5.938 r_rigid_bond_restr 3.609 r_dihedral_angle_other_3_deg 3.319 r_angle_refined_deg 1.8 r_angle_other_deg 0.617 r_symmetry_nbd_refined 0.343 r_nbd_refined 0.219 r_nbd_other 0.214 r_symmetry_xyhbond_nbd_refined 0.212 r_symmetry_nbd_other 0.204 r_nbtor_refined 0.181 r_xyhbond_nbd_refined 0.179 r_symmetry_nbtor_other 0.088 r_chiral_restr 0.085 r_symmetry_xyhbond_nbd_other 0.07 r_bond_refined_d 0.009 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4702 Nucleic Acid Atoms Solvent Atoms 481 Heterogen Atoms 96
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing