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SARS-CoV-2 Main Protease complexed with (1R)-N-(3-chlorophenyl)-3-oxo-N-[4-(2-oxopyrrolidin-1-yl)phenyl]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, HANGING DROP 7.5 293 0.2M NaFORMATE pH7.5, 20% PEG 3350 then soaking with inhibitor (DMSO) and cryo-protected with 10% Glycerol
Crystal Properties Matthews coefficient Solvent content 2.02 39.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.879 α = 114.926 b = 53.72 β = 100.263 c = 63.589 γ = 90.02
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 2022-09-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 2 0.980117 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 1.49 48.589 94.4 0.167 0.236 0.167 0.972 6.8 3.6 81151 14.66
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 1.49 1.52 0.936 5.913 4.181 0.101 2.8
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 1.493 48.589 81149 4023 94.537 0.183 0.1813 0.1901 0.2199 0.2239 17.029
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] -0.381 0.202 -0.039 -1.071 0.238 0.812
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.09 r_dihedral_angle_3_deg 14.879 r_dihedral_angle_2_deg 12.168 r_dihedral_angle_1_deg 7.433 r_angle_refined_deg 2.036 r_angle_other_deg 0.689 r_symmetry_nbd_refined 0.297 r_symmetry_xyhbond_nbd_refined 0.242 r_nbd_other 0.24 r_nbd_refined 0.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.09 r_dihedral_angle_3_deg 14.879 r_dihedral_angle_2_deg 12.168 r_dihedral_angle_1_deg 7.433 r_angle_refined_deg 2.036 r_angle_other_deg 0.689 r_symmetry_nbd_refined 0.297 r_symmetry_xyhbond_nbd_refined 0.242 r_nbd_other 0.24 r_nbd_refined 0.22 r_xyhbond_nbd_refined 0.199 r_symmetry_nbd_other 0.198 r_nbtor_refined 0.185 r_chiral_restr 0.109 r_symmetry_nbtor_other 0.085 r_bond_refined_d 0.015 r_gen_planes_refined 0.014 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4712 Nucleic Acid Atoms Solvent Atoms 571 Heterogen Atoms 85
Software Software Software Name Purpose REFMAC refinement Aimless data scaling MOLREP phasing MxCuBE data collection XDS data reduction