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Crystal Structure of SARS-CoV-2 Main protease 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 2.48 50.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.319 α = 90 b = 97.536 β = 90 c = 102.327 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 SIRUS BEAMLINE MANACA 0.977180 LNLS SIRUS 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 2.129 70.701 98.6 0.99 8.6 5.1 37960
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 2.129 2.206 0.763 2.3
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 2.129 70.701 37959 1898 98.633 0.191 0.1891 0.189 0.2295 0.2295 34.824
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] -1.906 2.956 -1.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.991 r_dihedral_angle_4_deg 20.551 r_dihedral_angle_3_deg 14.788 r_dihedral_angle_1_deg 7.935 r_lrange_it 6.677 r_lrange_other 6.652 r_scangle_it 4.976 r_scangle_other 4.976 r_mcangle_other 3.808 r_mcangle_it 3.807
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.991 r_dihedral_angle_4_deg 20.551 r_dihedral_angle_3_deg 14.788 r_dihedral_angle_1_deg 7.935 r_lrange_it 6.677 r_lrange_other 6.652 r_scangle_it 4.976 r_scangle_other 4.976 r_mcangle_other 3.808 r_mcangle_it 3.807 r_scbond_it 3.28 r_scbond_other 3.279 r_mcbond_it 2.585 r_mcbond_other 2.583 r_angle_refined_deg 1.55 r_angle_other_deg 1.392 r_nbd_refined 0.203 r_symmetry_nbd_other 0.201 r_symmetry_xyhbond_nbd_other 0.2 r_xyhbond_nbd_refined 0.196 r_nbd_other 0.191 r_symmetry_xyhbond_nbd_refined 0.172 r_nbtor_refined 0.17 r_symmetry_nbd_refined 0.158 r_symmetry_nbtor_other 0.083 r_chiral_restr 0.069 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 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 259 Heterogen Atoms 82
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing