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Crystal structure of the SARS-CoV-2 (COVID-19) main protease in complex with inhibitor Jun9-57-3R
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7KX5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 25 % 3350, 0.2 M AmSO4, 0.1 M HEPES 7.5
Crystal Properties Matthews coefficient Solvent content 1.97 37.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.42 α = 90 b = 53.43 β = 101.37 c = 112.031 γ = 90
Symmetry Space Group I 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 PILATUS3 6M 2021-02-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97890 APS 19-ID
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 2.25 50 92.4 0.071 0.087 0.05 0.994 7.6 2.7 11614
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 2.25 2.32 95.4 0.709 0.865 0.488 0.643 2.8
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 7KX5 2.25 48.05 11011 597 91.85 0.2151 0.2138 0.2187 0.241 0.242 RANDOM 53.388
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] -2.54 0.71 -0.75 2.78
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.263 r_dihedral_angle_4_deg 19.9 r_dihedral_angle_3_deg 17.813 r_dihedral_angle_1_deg 7.904 r_angle_refined_deg 1.62 r_angle_other_deg 1.312 r_chiral_restr 0.065 r_bond_refined_d 0.011 r_gen_planes_refined 0.008 r_bond_other_d 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.263 r_dihedral_angle_4_deg 19.9 r_dihedral_angle_3_deg 17.813 r_dihedral_angle_1_deg 7.904 r_angle_refined_deg 1.62 r_angle_other_deg 1.312 r_chiral_restr 0.065 r_bond_refined_d 0.011 r_gen_planes_refined 0.008 r_bond_other_d 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2326 Nucleic Acid Atoms Solvent Atoms 22 Heterogen Atoms 45
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction iMOSFLM data reduction MOLREP phasing