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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 10% PEG6000, 0.1M di-ammonium phosphate, 0.1M Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.95 58.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.474 α = 90 b = 242.866 β = 111.32 c = 105.222 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 IMAGE PLATE RIGAKU RAXIS IV 2005-08-25 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 93.8 0.082 11.1 100306
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 92.8 0.235 3.9 18951
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 45.45 100442 95388 5054 93.79 0.22496 0.22116 0.2524 0.2959 0.3118 RANDOM 14.606
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] 3.07 1.4 -2.5 0.45
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.041 r_dihedral_angle_3_deg 19.813 r_dihedral_angle_4_deg 18.513 r_dihedral_angle_1_deg 9.927 r_scangle_it 1.941 r_angle_refined_deg 1.532 r_scbond_it 1.218 r_mcangle_it 0.851 r_mcbond_it 0.485 r_symmetry_vdw_refined 0.344
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.041 r_dihedral_angle_3_deg 19.813 r_dihedral_angle_4_deg 18.513 r_dihedral_angle_1_deg 9.927 r_scangle_it 1.941 r_angle_refined_deg 1.532 r_scbond_it 1.218 r_mcangle_it 0.851 r_mcbond_it 0.485 r_symmetry_vdw_refined 0.344 r_nbtor_refined 0.312 r_nbd_refined 0.231 r_symmetry_hbond_refined 0.181 r_xyhbond_nbd_refined 0.169 r_chiral_restr 0.098 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 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 26133 Nucleic Acid Atoms Solvent Atoms 76 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement CrystalClear data collection PHASER phasing