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Crystal structures of high affinity human T-cell receptors bound to pMHC reveal native diagonal binding geometry
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2F53
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 293 85 MM HEPES, 8.5% ISO-PROPANOL, 17% PEG4000, 15% GLYCEROL, PH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 7.50
Crystal Properties Matthews coefficient Solvent content 2.46 50.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.59 α = 90 b = 52.325 β = 98.13 c = 118.932 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 CCD ADSC QUANTUM 4 MIRROR 2004-06-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SRS BEAMLINE PX14.2 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 2.2 24.805 99.3 0.145 0.145 4.3 3.8 46229
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 2.2 2.32 99.5 0.51 0.51 1.5 3.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 2F53 2.2 24.8 43884 2332 99.26 0.16941 0.16532 0.1691 0.24456 0.2447 RANDOM 14.825
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] 0.19 2.2 0.8 -0.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 24.07 r_scangle_it 9.998 r_dihedral_angle_3_deg 8.655 r_scbond_it 7.846 r_dihedral_angle_4_deg 7.687 r_mcangle_it 5.386 r_mcbond_it 4.324 r_dihedral_angle_1_deg 2.031 r_angle_refined_deg 1.711 r_mcbond_other 1.372
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 24.07 r_scangle_it 9.998 r_dihedral_angle_3_deg 8.655 r_scbond_it 7.846 r_dihedral_angle_4_deg 7.687 r_mcangle_it 5.386 r_mcbond_it 4.324 r_dihedral_angle_1_deg 2.031 r_angle_refined_deg 1.711 r_mcbond_other 1.372 r_angle_other_deg 0.952 r_symmetry_hbond_refined 0.271 r_xyhbond_nbd_other 0.267 r_symmetry_vdw_refined 0.235 r_xyhbond_nbd_refined 0.221 r_nbd_other 0.2 r_symmetry_vdw_other 0.199 r_nbd_refined 0.19 r_nbtor_refined 0.183 r_chiral_restr 0.103 r_nbtor_other 0.09 r_metal_ion_refined 0.052 r_bond_refined_d 0.016 r_gen_planes_refined 0.005 r_bond_other_d 0.003 r_gen_planes_other 0.001 r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6556 Nucleic Acid Atoms Solvent Atoms 675 Heterogen Atoms 113
Software Software Software Name Purpose SCALA data scaling AMoRE phasing REFMAC refinement PDB_EXTRACT data extraction MOSFLM data reduction