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SARS CoV-2 PLpro in complex with ubiquitin propargylamide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6WRH PDB entries 6WRH & 5OHK experimental model PDB 5OHK PDB entries 6WRH & 5OHK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 30% PEG4000, 0.2 M sodium acetate, 0.1 M Tris chloride, pH 8.5
Crystal Properties Matthews coefficient Solvent content 2.61 52.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.988 α = 90 b = 144.413 β = 90 c = 49.597 γ = 90
Symmetry Space Group P 21 21 2
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 EIGER X 16M 2020-05-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.9537 Australian Synchrotron MX2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.7 48.3 98.1 0.152 0.991 6.8 4.6 13062 50.43
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.7 2.83 98.9 1.054 0.508 4.7
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 entries 6WRH & 5OHK 2.7 48.3 1.33 13004 1305 96.86 0.2146 0.2096 0.2114 0.2599 0.2607 58.05
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 14.0093 f_angle_d 0.6635 f_chiral_restr 0.0441 f_plane_restr 0.0039 f_bond_d 0.0024
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2976 Nucleic Acid Atoms Solvent Atoms 32 Heterogen Atoms 1
Software Software Software Name Purpose PHENIX refinement XDS data processing Aimless data scaling Coot model building PHASER phasing XDS data reduction