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KRAS-specific 24-246 TCR in complex with HLA-C*01:02 presenting KRAS G12V 9mer peptide (11-AVGVGKSAL-19)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2BNQ TCR beta chain experimental model PDB 8ZO4 TCR alpha chain experimental model PDB 7DUU pHLA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 18% PEG 4000, 0.1 M TRIS pH 7.5, 0.1 M magnesium chloride
Crystal Properties Matthews coefficient Solvent content 2.57 52.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.007 α = 90 b = 62.706 β = 103.97 c = 127.012 γ = 90
Symmetry Space Group P 1 21 1
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 2025-05-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 1.05965 PETRA III, EMBL c/o DESY P13 (MX1)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.98 44.85 99.4 0.11 0.1 0.923 6.4 3.8 70121
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.98 2.03 1.339 0.7 3.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 THROUGHOUT 1.98 44.81 66490 3554 98.93 0.26124 0.25981 0.2453 0.28828 0.271 RANDOM 35.084
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] 3.91 5.19 6.29 -10.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.244 r_dihedral_angle_1_deg 6.246 r_dihedral_angle_2_deg 3.444 r_long_range_B_refined 3.193 r_long_range_B_other 3.193 r_mcangle_it 1.977 r_mcangle_other 1.976 r_scangle_other 1.669 r_mcbond_it 1.145 r_mcbond_other 1.145
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.244 r_dihedral_angle_1_deg 6.246 r_dihedral_angle_2_deg 3.444 r_long_range_B_refined 3.193 r_long_range_B_other 3.193 r_mcangle_it 1.977 r_mcangle_other 1.976 r_scangle_other 1.669 r_mcbond_it 1.145 r_mcbond_other 1.145 r_scbond_it 0.98 r_scbond_other 0.98 r_angle_refined_deg 0.833 r_angle_other_deg 0.328 r_chiral_restr 0.041 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_dihedral_angle_4_deg 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6191 Nucleic Acid Atoms Solvent Atoms 67 Heterogen Atoms 83
Software Software Software Name Purpose REFMAC refinement xia2 data scaling xia2 data reduction PHASER phasing PDB_EXTRACT data extraction