☰ Navigation Tabs
Crystal Structure of SARS-CoV-2 Main protease G143S 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 2.61 52.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.686 α = 90 b = 102.808 β = 91.289 c = 101.554 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 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 1.66 101.53 46.1 0.968 3.7 3.2 74929
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 1.66 1.72 0.463
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 1.664 101.528 74928 3690 46.108 0.21 0.2077 0.2078 0.2506 0.2507 19.413
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] -1.973 -0.318 -3.408 5.381
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.36 r_dihedral_angle_4_deg 18.383 r_dihedral_angle_3_deg 16.949 r_dihedral_angle_1_deg 8.792 r_lrange_it 6.285 r_lrange_other 6.061 r_mcangle_it 2.264 r_mcangle_other 2.264 r_scangle_it 2.225 r_scangle_other 2.225
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.36 r_dihedral_angle_4_deg 18.383 r_dihedral_angle_3_deg 16.949 r_dihedral_angle_1_deg 8.792 r_lrange_it 6.285 r_lrange_other 6.061 r_mcangle_it 2.264 r_mcangle_other 2.264 r_scangle_it 2.225 r_scangle_other 2.225 r_angle_refined_deg 1.973 r_mcbond_it 1.484 r_mcbond_other 1.484 r_scbond_it 1.475 r_scbond_other 1.475 r_angle_other_deg 1.254 r_xyhbond_nbd_refined 0.415 r_symmetry_xyhbond_nbd_refined 0.395 r_symmetry_nbd_refined 0.265 r_nbd_other 0.235 r_nbd_refined 0.218 r_symmetry_nbd_other 0.208 r_symmetry_xyhbond_nbd_other 0.191 r_nbtor_refined 0.165 r_xyhbond_nbd_other 0.149 r_chiral_restr 0.091 r_symmetry_nbtor_other 0.083 r_bond_refined_d 0.015 r_gen_planes_refined 0.009 r_bond_other_d 0.003 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9356 Nucleic Acid Atoms Solvent Atoms 639 Heterogen Atoms 144
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing