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Crystal structure of SARS-CoV-2 main protease G143S 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 0.1 M Tris pH 8.5, 3.0 M Sodium chloride
Crystal Properties Matthews coefficient Solvent content 2.76 55.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.395 α = 90 b = 207.65 β = 90 c = 104.052 γ = 90
Symmetry Space Group P 21 21 2
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 1.9 93.01 99.9 0.213 0.998 13.9 12.5 115699
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 1.9 1.93 1.22 0.462 2.2
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 1.97 73.604 103818 5227 99.83 0.207 0.2051 0.2038 0.2468 0.2543 29.573
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] 3.519 -8.087 4.568
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 20.25 r_lrange_other 19.858 r_lrange_it 19.856 r_dihedral_angle_6_deg 14.718 r_dihedral_angle_3_deg 13.271 r_scangle_it 11.258 r_scangle_other 11.257 r_mcangle_it 10.785 r_mcangle_other 10.785 r_rigid_bond_restr 8.394
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 20.25 r_lrange_other 19.858 r_lrange_it 19.856 r_dihedral_angle_6_deg 14.718 r_dihedral_angle_3_deg 13.271 r_scangle_it 11.258 r_scangle_other 11.257 r_mcangle_it 10.785 r_mcangle_other 10.785 r_rigid_bond_restr 8.394 r_scbond_other 7.89 r_scbond_it 7.889 r_mcbond_it 7.389 r_mcbond_other 7.387 r_dihedral_angle_1_deg 6.954 r_dihedral_angle_other_3_deg 2.995 r_angle_refined_deg 1.543 r_angle_other_deg 0.542 r_symmetry_xyhbond_nbd_refined 0.273 r_symmetry_nbd_refined 0.254 r_nbd_other 0.246 r_nbd_refined 0.216 r_symmetry_nbd_other 0.199 r_nbtor_refined 0.18 r_xyhbond_nbd_refined 0.143 r_symmetry_nbtor_other 0.084 r_symmetry_xyhbond_nbd_other 0.083 r_ncsr_local_group_4 0.082 r_chiral_restr 0.077 r_ncsr_local_group_1 0.076 r_ncsr_local_group_5 0.075 r_ncsr_local_group_3 0.073 r_ncsr_local_group_6 0.071 r_ncsr_local_group_2 0.066 r_xyhbond_nbd_other 0.026 r_bond_refined_d 0.008 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 9476 Nucleic Acid Atoms Solvent Atoms 311 Heterogen Atoms 264
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing