☰ Navigation Tabs
Crystal structure of the SARS-CoV-2 (COVID-19) main protease in complex with inhibitor Jun9-62-2R
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% PEG 3350, 0.2 M AmSO4, 0.1 M HEPES 7.5
Crystal Properties Matthews coefficient Solvent content 1.99 38.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 114.27 α = 90 b = 53.26 β = 102.82 c = 45.46 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 2021-04-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.0 APS 22-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 2.3 48.1 76.7 0.088 0.104 0.052 0.993 7.2 2.9 9032
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 2.3 2.38 82.2 0.423 0.495 0.25 0.736 2.9
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 2.3 48 8598 434 75.23 0.1992 0.198 0.2044 0.2225 0.2344 RANDOM 41.024
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] 0.76 -0.21 0.25 -0.83
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.117 r_dihedral_angle_3_deg 15.899 r_dihedral_angle_4_deg 14.507 r_dihedral_angle_1_deg 7.904 r_angle_refined_deg 1.544 r_angle_other_deg 1.279 r_chiral_restr 0.063 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.117 r_dihedral_angle_3_deg 15.899 r_dihedral_angle_4_deg 14.507 r_dihedral_angle_1_deg 7.904 r_angle_refined_deg 1.544 r_angle_other_deg 1.279 r_chiral_restr 0.063 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2352 Nucleic Acid Atoms Solvent Atoms 7 Heterogen Atoms 52
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction iMOSFLM data reduction MOLREP phasing