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Crystal Structure of SARS-CoV-2 Main protease A193T mutant in complex with Nirmatrelvir
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7MBG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 293 0.1 M MES, pH 6.7, 5% v/v DMSO, 8% w/v PEG4000, 30% w/v PEG400
Crystal Properties Matthews coefficient Solvent content 2.6 52.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.989 α = 90 b = 99.979 β = 90 c = 103.638 γ = 90
Symmetry Space Group P 21 21 21
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 2M 2022-04-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON LNLS SIRIUS BEAMLINE MANACA 0.977180 LNLS SIRIUS MANACA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.96 72.06 58.7 0.991 7.8 7.8 29962
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.96 2.03 0.253
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 7mbg 1.961 72.058 29962 1458 58.32 0.203 0.2007 0.2006 0.2419 0.2419 34.182
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] 0.012 0.189 -0.201
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.765 r_dihedral_angle_4_deg 19.574 r_dihedral_angle_3_deg 15.479 r_lrange_it 7.912 r_lrange_other 7.905 r_dihedral_angle_1_deg 7.68 r_scangle_it 4.428 r_scangle_other 4.428 r_mcangle_it 3.458 r_mcangle_other 3.458
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.765 r_dihedral_angle_4_deg 19.574 r_dihedral_angle_3_deg 15.479 r_lrange_it 7.912 r_lrange_other 7.905 r_dihedral_angle_1_deg 7.68 r_scangle_it 4.428 r_scangle_other 4.428 r_mcangle_it 3.458 r_mcangle_other 3.458 r_scbond_it 2.81 r_scbond_other 2.81 r_mcbond_it 2.15 r_mcbond_other 2.147 r_angle_refined_deg 1.417 r_angle_other_deg 1.282 r_nbd_other 0.339 r_symmetry_xyhbond_nbd_refined 0.32 r_symmetry_xyhbond_nbd_other 0.318 r_symmetry_nbd_refined 0.277 r_xyhbond_nbd_refined 0.22 r_nbd_refined 0.206 r_symmetry_nbd_other 0.202 r_nbtor_refined 0.165 r_symmetry_nbtor_other 0.079 r_chiral_restr 0.061 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4691 Nucleic Acid Atoms Solvent Atoms 175 Heterogen Atoms 90
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing