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Crystal structure of SARS-CoV-2 main protease H172Y 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, SITTING DROP 289 2% v/v TacsimateTM pH 6.0, 0.1 M BIS-TRIS pH 6.5, 20% w/v Polyethylene glycol 3,350
Crystal Properties Matthews coefficient Solvent content 2.08 40.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.953 α = 90 b = 106.45 β = 102.896 c = 54.036 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 2.267 53.225 95.5 0.121 0.997 13.2 6.4 23949
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 2.27 2.34 0.876 0.818 2.8
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 2.267 53.225 23605 1222 94.414 0.174 0.1704 0.1795 0.2402 0.2436 34.348
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] -0.479 0.911 -0.954 0.919
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 15.586 r_dihedral_angle_3_deg 14.921 r_dihedral_angle_6_deg 14.276 r_lrange_it 8.579 r_lrange_other 8.577 r_dihedral_angle_1_deg 6.499 r_scangle_it 5.573 r_scangle_other 5.572 r_mcangle_it 4.718 r_mcangle_other 4.717
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 15.586 r_dihedral_angle_3_deg 14.921 r_dihedral_angle_6_deg 14.276 r_lrange_it 8.579 r_lrange_other 8.577 r_dihedral_angle_1_deg 6.499 r_scangle_it 5.573 r_scangle_other 5.572 r_mcangle_it 4.718 r_mcangle_other 4.717 r_scbond_it 3.705 r_scbond_other 3.704 r_dihedral_angle_other_3_deg 3.347 r_mcbond_it 3.183 r_mcbond_other 3.17 r_angle_refined_deg 1.379 r_angle_other_deg 0.51 r_symmetry_xyhbond_nbd_refined 0.233 r_nbd_refined 0.206 r_symmetry_nbd_other 0.2 r_symmetry_nbd_refined 0.196 r_nbd_other 0.194 r_nbtor_refined 0.181 r_xyhbond_nbd_refined 0.166 r_ncsr_local_group_1 0.12 r_symmetry_nbtor_other 0.081 r_chiral_restr 0.077 r_symmetry_xyhbond_nbd_other 0.061 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4836 Nucleic Acid Atoms Solvent Atoms 238 Heterogen Atoms 96
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing