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Crystal structure of JDI TCR in complex with HLA-A*11:01 bound to KRAS G12D peptide (VVVGADGVGK)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4UQ2 4UQ2, 4JRX, 4X6B experimental model PDB 4JRX 4UQ2, 4JRX, 4X6B experimental model PDB 4X6B 4UQ2, 4JRX, 4X6B
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.2 M ammonium sulfate, 0.1 M Tris pH 8.5, 20 % PEG 8000
Crystal Properties Matthews coefficient Solvent content 3.55 65.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 208.366 α = 90 b = 208.366 β = 90 c = 124.671 γ = 90
Symmetry Space Group P 41 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 PILATUS 6M-F 2017-07-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.9159 Diamond I04-1
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 3.41 147.77 99.98 0.135 0.138 0.026 1 18.7 28.5 38015
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 3.41 3.47 99.52 2.603 2.68 0.622 0.618 1.4 17.5
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4UQ2, 4JRX, 4X6B 3.41 147.77 36110 1864 99.87 0.22912 0.22783 0.2537 0.2216 RANDOM 79.926
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] -0.33 -0.33 0.65
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.391 r_dihedral_angle_3_deg 16 r_dihedral_angle_4_deg 12.079 r_dihedral_angle_1_deg 5.992 r_angle_refined_deg 1.185 r_angle_other_deg 1.04 r_chiral_restr 0.034 r_bond_refined_d 0.002 r_gen_planes_refined 0.002 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.391 r_dihedral_angle_3_deg 16 r_dihedral_angle_4_deg 12.079 r_dihedral_angle_1_deg 5.992 r_angle_refined_deg 1.185 r_angle_other_deg 1.04 r_chiral_restr 0.034 r_bond_refined_d 0.002 r_gen_planes_refined 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12801 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement DIALS data reduction DIALS data scaling PHASER phasing