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Crystal structure of SARS-CoV-2 Mpro with compound C5
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 2.57 52.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.29 α = 90 b = 102.64 β = 100.25 c = 102.2 γ = 90
Symmetry Space Group P 1 21 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 S 6M 2021-08-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08B1-1 1.1806 CLSI 08B1-1
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 1.8 45.75 99.9 0.132 0.143 0.055 0.998 8.5 6.7 126257
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 1.8 1.83 100 2.146 2.321 0.876 0.475 6.8
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 7JOY 1.8 45.75 119897 6360 99.91 0.2138 0.2121 0.2229 0.2453 0.2476 RANDOM 31.132
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] 0.41 0.8 -0.3 -0.37
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.369 r_dihedral_angle_4_deg 19.597 r_dihedral_angle_3_deg 15.486 r_dihedral_angle_1_deg 7.481 r_angle_refined_deg 1.789 r_angle_other_deg 1.479 r_chiral_restr 0.089 r_bond_refined_d 0.013 r_gen_planes_refined 0.01 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.369 r_dihedral_angle_4_deg 19.597 r_dihedral_angle_3_deg 15.486 r_dihedral_angle_1_deg 7.481 r_angle_refined_deg 1.789 r_angle_other_deg 1.479 r_chiral_restr 0.089 r_bond_refined_d 0.013 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9430 Nucleic Acid Atoms Solvent Atoms 666 Heterogen Atoms 120
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction xia2 data reduction xia2 data scaling PHASER phasing