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SARS-CoV-2 Main Protease (Mpro) in complex with nirmatrelvir alkyne
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6YB7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 11% (v/v) PEG 4K, 5% (v/v) DMSO, 0.1 M MES pH 6.5
Crystal Properties Matthews coefficient Solvent content 2.31 46.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.037 α = 90 b = 64.392 β = 90 c = 104.952 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 X CdTe 2M 2022-07-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE VMXm 0.58124 Diamond VMXm
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.89 22.48 79.1 0.543 0.569 0.162 0.984 7.6 16.4 20055
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.89 1.94 7.222 7.519 2.055 0.475 22.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 6yb7 1.893 22.48 19991 995 78.029 0.184 0.1824 0.1949 0.2234 0.2384 30.792
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] -0.679 0.232 0.447
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.537 r_dihedral_angle_3_deg 13.417 r_lrange_other 10.184 r_lrange_it 10.18 r_scangle_it 8.633 r_scangle_other 8.631 r_dihedral_angle_2_deg 7.264 r_dihedral_angle_1_deg 7.236 r_scbond_it 6.502 r_scbond_other 6.499
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.537 r_dihedral_angle_3_deg 13.417 r_lrange_other 10.184 r_lrange_it 10.18 r_scangle_it 8.633 r_scangle_other 8.631 r_dihedral_angle_2_deg 7.264 r_dihedral_angle_1_deg 7.236 r_scbond_it 6.502 r_scbond_other 6.499 r_mcangle_other 6.301 r_mcangle_it 6.291 r_mcbond_it 4.633 r_mcbond_other 4.62 r_angle_refined_deg 1.419 r_angle_other_deg 0.472 r_nbd_refined 0.206 r_symmetry_nbd_other 0.184 r_nbtor_refined 0.172 r_xyhbond_nbd_refined 0.142 r_symmetry_xyhbond_nbd_refined 0.122 r_nbd_other 0.114 r_symmetry_nbtor_other 0.078 r_chiral_restr 0.069 r_symmetry_nbd_refined 0.067 r_dihedral_angle_other_1_deg 0.007 r_gen_planes_refined 0.007 r_bond_refined_d 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2359 Nucleic Acid Atoms Solvent Atoms 83 Heterogen Atoms 35
Software Software Software Name Purpose REFMAC refinement PDB-REDO refinement Aimless data scaling xia2.multiplex data scaling MOLREP phasing xia2.multiplex data reduction