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Crystal structure of SARS-CoV-2 main protease P168 deletion 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 Sodium citrate tribasic dihydrate pH 5.5, 16% w/v Polyethylene glycol 8,000
Crystal Properties Matthews coefficient Solvent content 2.07 40.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 114.267 α = 90 b = 53.048 β = 102.736 c = 46.225 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 PILATUS 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 1.7 55.73 99.1 0.115 0.998 12.8 6.3 29555
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 1.7 1.73 0.848 0.513 2.1
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.7 55.728 29526 1525 98.944 0.18 0.1776 0.1848 0.2305 0.2397 RANDOM 19.042
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] 3.613 -0.517 -2.707 -0.61
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 18.21 r_dihedral_angle_2_deg 16.615 r_dihedral_angle_6_deg 14.702 r_lrange_other 13.975 r_dihedral_angle_3_deg 12.58 r_dihedral_angle_1_deg 7.609 r_scangle_it 7.044 r_scangle_other 7.042 r_mcangle_other 6.307 r_mcangle_it 6.305
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 18.21 r_dihedral_angle_2_deg 16.615 r_dihedral_angle_6_deg 14.702 r_lrange_other 13.975 r_dihedral_angle_3_deg 12.58 r_dihedral_angle_1_deg 7.609 r_scangle_it 7.044 r_scangle_other 7.042 r_mcangle_other 6.307 r_mcangle_it 6.305 r_scbond_it 4.594 r_scbond_other 4.592 r_rigid_bond_restr 4.134 r_mcbond_it 4.087 r_mcbond_other 4.013 r_dihedral_angle_other_3_deg 2.02 r_angle_refined_deg 1.522 r_angle_other_deg 0.531 r_nbd_refined 0.227 r_symmetry_nbd_other 0.201 r_nbtor_refined 0.182 r_nbd_other 0.179 r_xyhbond_nbd_refined 0.154 r_symmetry_nbd_refined 0.112 r_symmetry_xyhbond_nbd_other 0.1 r_symmetry_xyhbond_nbd_refined 0.095 r_symmetry_nbtor_other 0.083 r_chiral_restr 0.076 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 2322 Nucleic Acid Atoms Solvent Atoms 222 Heterogen Atoms 45
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing