☰ Navigation Tabs
Crystal structure of SARS-CoV-2 main protease S144A 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 0.2 M Ammonium sulfate, 0.1 M Tris pH 8.5, 25% w/v Polyethylene glycol 3,350
Crystal Properties Matthews coefficient Solvent content 2.09 41.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.581 α = 90 b = 107.058 β = 102.914 c = 54.318 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 53.53 91.6 0.188 0.991 7.3 6.3 33515
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 2.05 1.221 0.619 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 2 53.529 33427 1714 91.473 0.187 0.1842 0.191 0.2389 0.2464 30.893
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] 0.821 0.5 -0.066 -0.891
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 23.208 r_dihedral_angle_6_deg 14.666 r_dihedral_angle_3_deg 13.596 r_lrange_it 8.669 r_lrange_other 8.66 r_dihedral_angle_1_deg 7.11 r_scangle_it 5.473 r_scangle_other 5.472 r_mcangle_it 4.448 r_mcangle_other 4.448
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 23.208 r_dihedral_angle_6_deg 14.666 r_dihedral_angle_3_deg 13.596 r_lrange_it 8.669 r_lrange_other 8.66 r_dihedral_angle_1_deg 7.11 r_scangle_it 5.473 r_scangle_other 5.472 r_mcangle_it 4.448 r_mcangle_other 4.448 r_scbond_it 3.661 r_scbond_other 3.66 r_mcbond_it 2.985 r_mcbond_other 2.974 r_dihedral_angle_other_3_deg 1.889 r_angle_refined_deg 1.521 r_angle_other_deg 0.522 r_nbd_other 0.243 r_symmetry_xyhbond_nbd_refined 0.222 r_nbd_refined 0.209 r_symmetry_nbd_refined 0.204 r_symmetry_nbd_other 0.196 r_nbtor_refined 0.182 r_xyhbond_nbd_refined 0.145 r_symmetry_nbtor_other 0.085 r_ncsr_local_group_1 0.084 r_chiral_restr 0.075 r_symmetry_xyhbond_nbd_other 0.045 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4621 Nucleic Acid Atoms Solvent Atoms 239 Heterogen Atoms 204
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing