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The crystal structure of SARS-CoV-2 3CL protease in complex with compound 3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6Y2E
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.1 M BIS-TRIS pH 6.5, 2.0 M Ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 2.27 45.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.468 α = 90 b = 99.229 β = 108.05 c = 58.883 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 RIGAKU HyPix-6000HE 2021-04-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-X 1.54178
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 55.99 99.8 0.06 0.067 0.029 0.997 20.5 5.2 56021
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 1.84 100 0.429 0.513 0.275 0.808 3.4
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 6Y2E 1.8 55.99 52687 2669 98.68 0.2267 0.2241 0.2277 0.279 0.2828 RANDOM 17.802
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] -0.45 -0.86 0.3 0.58
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.329 r_dihedral_angle_3_deg 13.995 r_dihedral_angle_4_deg 11.069 r_dihedral_angle_1_deg 6.432 r_angle_refined_deg 1.796 r_chiral_restr 0.127 r_bond_refined_d 0.018 r_gen_planes_refined 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4509 Nucleic Acid Atoms Solvent Atoms 350 Heterogen Atoms 74
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction CrysalisPro data reduction MOLREP phasing