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Crystal structure of Mpro in complex with inhibitor CDD-1713
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7K3T PDB entry 7K3T
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 298 20% PEG3350, 0.2 M sodium acetate
Crystal Properties Matthews coefficient Solvent content 1.99 38.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 114.742 α = 90 b = 53.71 β = 101.164 c = 44.49 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 298 CCD ADSC QUANTUM 315r 2020-10-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.1 1.11 ALS 8.2.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) 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 1.787 33.871 99.43 0.126 0.076 6 4.1 25156 26.09
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.79 1.82 0.061
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE PDB entry 7K3T 1.79 33.87 1.34 25072 1260 99.1 0.2005 0.1982 0.1991 0.2449 0.246 30.03
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 6.9971 f_angle_d 1.0939 f_chiral_restr 0.0535 f_plane_restr 0.0131 f_bond_d 0.0075
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2367 Nucleic Acid Atoms Solvent Atoms 209 Heterogen Atoms 26
Software Software Software Name Purpose PHENIX refinement PHENIX refinement iMOSFLM data reduction Aimless data scaling PHASER phasing