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Germline-governed recognition of a cancer epitope by an immunodominant human T cell receptor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2F53 experimental model PDB 1AO7 experimental model PDB 2BCK experimental model PDB 2F53
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.4 293 23% PEG 550 MME, 0.1M TRIS, 15% Glycerol, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.21 61.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 120.898 α = 90 b = 120.898 β = 90 c = 81.98 γ = 90
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 4 Mirror 2007-08-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SRS BEAMLINE PX14.2 0.979 SRS PX14.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 3 48.65 99.6 0.164 0.164 4.512 3.4 23764 65.9
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3 3.16 100 0.737 0.737 1 3.4 3464
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 3 48.65 23740 1211 99.46 0.229 0.225 0.2326 0.304 0.3057 RANDOM 42.638
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] 1.3 1.3 -2.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 17.476 r_dihedral_angle_3_deg 8.917 r_dihedral_angle_4_deg 7.347 r_scangle_it 7.146 r_scbond_it 4.55 r_mcangle_it 3.233 r_dihedral_angle_1_deg 2.05 r_mcbond_it 1.769 r_angle_refined_deg 1.021 r_angle_other_deg 1.016
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 17.476 r_dihedral_angle_3_deg 8.917 r_dihedral_angle_4_deg 7.347 r_scangle_it 7.146 r_scbond_it 4.55 r_mcangle_it 3.233 r_dihedral_angle_1_deg 2.05 r_mcbond_it 1.769 r_angle_refined_deg 1.021 r_angle_other_deg 1.016 r_chiral_restr 0.074 r_bond_refined_d 0.015 r_gen_planes_refined 0.005 r_gen_planes_other 0.005 r_bond_other_d r_mcbond_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6583 Nucleic Acid Atoms Solvent Atoms 44 Heterogen Atoms 22
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction ADSC data collection