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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
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 295 10% PEG-2000 MME, 0.1M Tris, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.39 48.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 170.044 α = 90 b = 65.663 β = 90 c = 84.817 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 CCD ADSC QUANTUM 315 2005-07-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A 1.0 NSLS X29A
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 1.92 50 0.108 13.1 71032
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) 1.92 1.99 78.1 0.491 1.5 9536
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1FYT 1.92 44.31 69224 65728 3496 94.09 0.21032 0.20753 0.26453 0.2705 RANDOM 31.079
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] 0.6 -0.08 -0.52
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.07 r_dihedral_angle_3_deg 18.308 r_dihedral_angle_4_deg 14.843 r_dihedral_angle_1_deg 12.647 r_scangle_it 4.501 r_scbond_it 2.988 r_mcangle_it 2.025 r_angle_refined_deg 1.869 r_mcbond_it 1.241 r_nbtor_refined 0.306
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.07 r_dihedral_angle_3_deg 18.308 r_dihedral_angle_4_deg 14.843 r_dihedral_angle_1_deg 12.647 r_scangle_it 4.501 r_scbond_it 2.988 r_mcangle_it 2.025 r_angle_refined_deg 1.869 r_mcbond_it 1.241 r_nbtor_refined 0.306 r_symmetry_vdw_refined 0.273 r_nbd_refined 0.221 r_xyhbond_nbd_refined 0.155 r_symmetry_hbond_refined 0.149 r_chiral_restr 0.139 r_bond_refined_d 0.019 r_gen_planes_refined 0.01 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 6862 Nucleic Acid Atoms Solvent Atoms 243 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement PHASER phasing