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SARS-CoV-2 Main Protease (Mpro) in Complex with ML188
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6M03
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 23% (w/v) PEG 3350, Potassium Sodium Tartrate Tetrahydrate
Crystal Properties Matthews coefficient Solvent content 1.98 37.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 113.19 α = 90 b = 52.666 β = 102.83 c = 46.098 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 CCD RIGAKU SATURN 944 2020-11-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54178
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.39 30.16 87.91 0.06869 0.04542 0.995 12.33 3 9338
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.39 2.476 84.62 0.3126 0.2099 0.862 3.39
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 6M03 2.39 30.16 1.34 9337 467 87.97 0.2042 0.2012 0.261 0.2537 35.7691
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 15.253 f_angle_d 0.584 f_chiral_restr 0.041 f_bond_d 0.003 f_plane_restr 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2309 Nucleic Acid Atoms Solvent Atoms 100 Heterogen Atoms 63
Software Software Software Name Purpose HKL-3000 data scaling PHASER phasing PHENIX refinement Coot model building PDB_EXTRACT data extraction HKL-3000 data reduction