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Structural basis for recognition of mutant self by a tumor-specific, MHC class II-restricted TCR
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1FYT 1FYT, 1IAL experimental model PDB 1IAL 1FYT, 1IAL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 295 8% PEG6000, 0.1M di-ammonium phosphate, 0.1M Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 3.02 59.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.391 α = 90 b = 270.542 β = 90 c = 97.396 γ = 90
Symmetry Space Group C 2 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 IMAGE PLATE RIGAKU RAXIS IV 2005-08-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.8 50 92.8 0.091 10.7 26581
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) 2.8 2.94 91.9 0.513 3 5639
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 1FYT, 1IAL 2.8 41.91 26375 25046 1329 92.16 0.21051 0.20693 0.2418 0.27915 0.3004 RANDOM 62.8
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] -5.39 4.95 0.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.547 r_dihedral_angle_3_deg 21.109 r_dihedral_angle_4_deg 18.69 r_dihedral_angle_1_deg 10.92 r_scangle_it 2.944 r_angle_refined_deg 1.96 r_scbond_it 1.908 r_mcangle_it 1.278 r_mcbond_it 0.752 r_nbtor_refined 0.322
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.547 r_dihedral_angle_3_deg 21.109 r_dihedral_angle_4_deg 18.69 r_dihedral_angle_1_deg 10.92 r_scangle_it 2.944 r_angle_refined_deg 1.96 r_scbond_it 1.908 r_mcangle_it 1.278 r_mcbond_it 0.752 r_nbtor_refined 0.322 r_symmetry_vdw_refined 0.256 r_nbd_refined 0.253 r_xyhbond_nbd_refined 0.178 r_chiral_restr 0.117 r_symmetry_hbond_refined 0.043 r_bond_refined_d 0.019 r_gen_planes_refined 0.008 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6511 Nucleic Acid Atoms Solvent Atoms 40 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement CrystalClear data collection PHASER phasing