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Crystal structure of the SARS-CoV-2 Main Protease complexed with N-(pyridin-3-ylmethyl)thioformamide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7K3T
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.2M NaFormate, 20% PEG 3350, 10% Glycerol, 10% DMSO
Crystal Properties Matthews coefficient Solvent content 1.97 37.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 114.92 α = 90 b = 52.91 β = 102.88 c = 44.9 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 16M 2020-11-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.978564 SOLEIL PROXIMA 1
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 1.49 47.84 98.7 0.998 9.77 6.9 42066
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 1.49 1.59 91.9 0.51
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 7K3T 1.495 43.809 42065 2104 98.712 0.173 0.1706 0.1687 0.2132 0.2107 23.691
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] 0.473 -0.229 0.034 -0.364
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.03 r_dihedral_angle_4_deg 12.973 r_dihedral_angle_3_deg 12.37 r_dihedral_angle_1_deg 7.279 r_angle_refined_deg 1.675 r_angle_other_deg 1.458 r_dihedral_angle_other_3_deg 0.764 r_symmetry_nbd_refined 0.302 r_symmetry_xyhbond_nbd_refined 0.278 r_nbd_refined 0.233
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.03 r_dihedral_angle_4_deg 12.973 r_dihedral_angle_3_deg 12.37 r_dihedral_angle_1_deg 7.279 r_angle_refined_deg 1.675 r_angle_other_deg 1.458 r_dihedral_angle_other_3_deg 0.764 r_symmetry_nbd_refined 0.302 r_symmetry_xyhbond_nbd_refined 0.278 r_nbd_refined 0.233 r_symmetry_nbd_other 0.188 r_nbd_other 0.178 r_xyhbond_nbd_refined 0.171 r_nbtor_refined 0.17 r_chiral_restr 0.083 r_symmetry_nbtor_other 0.078 r_bond_refined_d 0.011 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2368 Nucleic Acid Atoms Solvent Atoms 216 Heterogen Atoms 44
Software Software Software Name Purpose REFMAC refinement Aimless data reduction Aimless data scaling MOLREP phasing XDS data processing