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Complex of T cell Receptor with HHAT Neoantigen Peptide 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 6.3 277 0.1 M sodium citrate, pH 6.3, 7.5% PEG6000, 0.2 M lithium nitrate
Crystal Properties Matthews coefficient Solvent content 3.23 61.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.31 α = 90 b = 86.507 β = 90 c = 238.78 γ = 90
Symmetry Space Group P 21 21 21
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 2019-07-30 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) R Merge I (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 2.69 50 99 0.113 0.121 0.042 0.98 16 7.8 35931 63.92
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.69 2.74 94.3 0.5 0.539 0.195 0.908 3.3 5.9
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 1TVH, 5JZI, & 5C0B 2.7 49.47 1.34 34958 1949 99.16 0.2214 0.2196 0.2243 0.2522 0.2556 73.93
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 23.4966 f_angle_d 0.7389 f_chiral_restr 0.0486 f_bond_d 0.0042 f_plane_restr 0.0035
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6728 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement PHENIX model building HKL-2000 data reduction HKL-2000 data scaling PHASER phasing