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Crystal structure of SARS-CoV-2 Mpro with compound C3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7JOY 7JOY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 293 0.1 M Tris pH 8, 15 % PEG 8000, 10 % ethylene glycol
Crystal Properties Matthews coefficient Solvent content 2.62 53.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.81 α = 74.59 b = 67.817 β = 79.39 c = 94.614 γ = 66.39
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 R 200K-A 2021-07-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.0332
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 2.1 46.71 96.1 0.1 0.125 0.074 0.995 3.2 2.7 77001
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 2.1 2.14 96.3 1.41 1.764 1.044 0.562 2.7
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 7JOY 2.1 46.71 72991 3772 95.77 0.2174 0.216 0.2263 0.2438 0.2502 RANDOM 57.963
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] 2.01 -2.75 3.31 -1.68 -0.23 -1.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.891 r_dihedral_angle_4_deg 18.125 r_dihedral_angle_3_deg 17.07 r_dihedral_angle_1_deg 7.365 r_angle_refined_deg 1.703 r_angle_other_deg 1.318 r_chiral_restr 0.074 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.891 r_dihedral_angle_4_deg 18.125 r_dihedral_angle_3_deg 17.07 r_dihedral_angle_1_deg 7.365 r_angle_refined_deg 1.703 r_angle_other_deg 1.318 r_chiral_restr 0.074 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9434 Nucleic Acid Atoms Solvent Atoms 312 Heterogen Atoms 124
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction CrysalisPro data reduction PHASER phasing