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Alpha-beta TCR Binding to Neoantigen KQWLVWLFL Presented by HLA-A206
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1TVH PDB entries 1TVH, 5JZI, & 5C0B experimental model PDB 5JZI PDB entries 1TVH, 5JZI, & 5C0B experimental model PDB 5C0B PDB entries 1TVH, 5JZI, & 5C0B
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 295.5 8 mg/mL protein, 12.5% PEG3350, 0.1 M MOPS, pH 7.0, 0.25 M lithium nitrate
Crystal Properties Matthews coefficient Solvent content 3.31 62.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 276.641 α = 90 b = 276.641 β = 90 c = 112.465 γ = 120
Symmetry Space Group P 61 2 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 2018-07-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.98 APS 24-ID-E
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim 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 3.04879832067 49.38 99.6 0.18 0.99 9.2 5.3 48454 58.6177609415
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.04879832067 3.1 99.9 1.19 0.538 1.6 5.2
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 FREE R-VALUE PDB entries 1TVH, 5JZI, & 5C0B 3.05 49.38 46045 1880 94.6940874036 0.195257806136 0.194273139606 0.1902 0.218829744142 0.2149 Random Selection 66.9632652374
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 18.0446626468 f_angle_d 0.679895973716 f_chiral_restr 0.0484355259885 f_plane_restr 0.00812282204008 f_bond_d 0.00317390782332
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13222 Nucleic Acid Atoms Solvent Atoms 32 Heterogen Atoms 30
Software Software Software Name Purpose PHENIX refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing