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SARS-CoV-2 ORF3a peptide in complex with TRAF3 TRAF domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4GHU ChainA of 4GHU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 293.15 13% PEG3350, 0.1 M Tris, pH 8.0, 0.25 M ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 3.71 66.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.35 α = 60.03 b = 83.75 β = 79.26 c = 83.8 γ = 83.8
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 6M 2021-03-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 1.033 APS 23-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.5 41.77 97.5 0.174 0.065 0.996 11.11 7.1 64645 55.89
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.56 94.3 2.329 0.928 0.505 1.72 6.3
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 4GHU 2.5 41.77 1.94 64627 3087 97.84 0.1991 0.1969 0.1971 0.2424 0.2418 62.56
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 5.9578 f_angle_d 0.9249 f_chiral_restr 0.0523 f_bond_d 0.0081 f_plane_restr 0.0079
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9201 Nucleic Acid Atoms Solvent Atoms 27 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement PHENIX refinement XDS data reduction XDS data scaling PHASER phasing