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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% Isopropanol, 17% PEG 4000, 15% Glycerol, pH 7.5, VAPOR DIFFUSION, temperature 293K, pH 7.50
Crystal Properties Matthews coefficient Solvent content 2.4 48.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.002 α = 90 b = 51.771 β = 98.24 c = 118.27 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 + MONOCHROMATOR 2005-07-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SRS BEAMLINE PX14.1 SRS PX14.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.887 117 69966
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 1.89 117.04 66411 3552 97.44 0.18071 0.17777 0.1813 0.23579 0.238 RANDOM 12.457
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] 1.29 1.52 0.3 -1.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 24.273 r_dihedral_angle_4_deg 10.558 r_dihedral_angle_3_deg 8.812 r_scangle_it 7.091 r_scbond_it 5.409 r_mcangle_it 3.544 r_mcbond_it 3.072 r_dihedral_angle_1_deg 2.817 r_angle_refined_deg 1.173 r_mcbond_other 0.86
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 24.273 r_dihedral_angle_4_deg 10.558 r_dihedral_angle_3_deg 8.812 r_scangle_it 7.091 r_scbond_it 5.409 r_mcangle_it 3.544 r_mcbond_it 3.072 r_dihedral_angle_1_deg 2.817 r_angle_refined_deg 1.173 r_mcbond_other 0.86 r_angle_other_deg 0.71 r_symmetry_hbond_refined 0.318 r_xyhbond_nbd_refined 0.23 r_symmetry_vdw_other 0.226 r_nbd_other 0.213 r_nbd_refined 0.196 r_xyhbond_nbd_other 0.191 r_nbtor_refined 0.187 r_symmetry_vdw_refined 0.185 r_nbtor_other 0.092 r_chiral_restr 0.088 r_metal_ion_refined 0.019 r_bond_refined_d 0.017 r_gen_planes_refined 0.01 r_bond_other_d 0.003 r_gen_planes_other 0.002 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 6568 Nucleic Acid Atoms Solvent Atoms 739 Heterogen Atoms 93
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction MOSFLM data reduction SCALA data scaling MOLREP phasing