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SARS-CoV-2 Main Protease in complex with with (1R)-N-(3-chlorophenyl)-N-[4-(2,4-dioxo-1H-pyrimidin-5-yl)phenyl]-3-oxo-indane-1-carboxamide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7NTT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 293 0.2 M Potassium chloride 20% (w/v) PEG 3350
Crystal Properties Matthews coefficient Solvent content 2 38.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 114.41 α = 90 b = 53.825 β = 100.805 c = 44.64 γ = 90
Symmetry Space Group C 1 2 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 EIGER X 9M 2024-02-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 2 0.980112 SOLEIL PROXIMA 2
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 1.696 48.592 99.7 0.07 0.084 0.046 0.999 12.6 6.2 29572 25.69
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 1.7 1.73 1.111 1.354 0.762 0.54 5.7
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 1.696 48.592 29571 1500 99.65 0.174 0.171 0.1687 0.2214 0.2208 23.119
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] 0.151 -0.557 1.01 -0.884
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.373 r_dihedral_angle_6_deg 14.636 r_dihedral_angle_3_deg 12.868 r_dihedral_angle_1_deg 7.42 r_lrange_it 7.364 r_lrange_other 7.301 r_scangle_it 5.557 r_scangle_other 5.556 r_scbond_it 3.844 r_scbond_other 3.843
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.373 r_dihedral_angle_6_deg 14.636 r_dihedral_angle_3_deg 12.868 r_dihedral_angle_1_deg 7.42 r_lrange_it 7.364 r_lrange_other 7.301 r_scangle_it 5.557 r_scangle_other 5.556 r_scbond_it 3.844 r_scbond_other 3.843 r_mcangle_it 3.16 r_mcangle_other 3.16 r_mcbond_it 2.373 r_mcbond_other 2.372 r_angle_refined_deg 1.944 r_angle_other_deg 0.68 r_xyhbond_nbd_refined 0.236 r_nbd_refined 0.216 r_nbd_other 0.21 r_symmetry_nbd_other 0.202 r_nbtor_refined 0.188 r_symmetry_nbd_refined 0.156 r_symmetry_xyhbond_nbd_refined 0.15 r_chiral_restr 0.1 r_symmetry_nbtor_other 0.087 r_bond_refined_d 0.01 r_gen_planes_refined 0.01 r_symmetry_xyhbond_nbd_other 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2349 Nucleic Acid Atoms Solvent Atoms 386 Heterogen Atoms 36
Software Software Software Name Purpose REFMAC refinement MxCuBE data collection Aimless data scaling MOLREP phasing XDS data reduction