☰ Navigation Tabs
Crystal Structures of High Affinity Human T-Cell Receptors Bound to pMHC RevealNative Diagonal Binding Geometry Unbound TCR Clone 5-1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2BNR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 291 85 mM Na HEPES buffer pH7.5, 8.5 % iso-propanol, 17% PEG 4000, 15% glycerol, pH 7.50, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.12 42.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.964 α = 90 b = 59.805 β = 90.94 c = 81.799 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) 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 30 97 0.139 0.139 3.9 3.2 20741
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 90.8 0.671 0.079 1.3 3.1 701
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 2BNR 2.2 30 19532 1064 0.21348 0.20919 0.2078 0.29484 0.2871 RANDOM 17.403
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] -0.97 1.45 -0.46 1.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 16.478 r_scangle_it 7.772 r_dihedral_angle_3_deg 5.8 r_scbond_it 5.795 r_dihedral_angle_4_deg 4.772 r_mcangle_it 4.102 r_mcbond_it 2.771 r_dihedral_angle_1_deg 1.269 r_angle_refined_deg 1.253 r_angle_other_deg 0.722
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 16.478 r_scangle_it 7.772 r_dihedral_angle_3_deg 5.8 r_scbond_it 5.795 r_dihedral_angle_4_deg 4.772 r_mcangle_it 4.102 r_mcbond_it 2.771 r_dihedral_angle_1_deg 1.269 r_angle_refined_deg 1.253 r_angle_other_deg 0.722 r_mcbond_other 0.668 r_symmetry_hbond_refined 0.265 r_nbd_other 0.215 r_xyhbond_nbd_refined 0.209 r_symmetry_vdw_refined 0.206 r_nbd_refined 0.204 r_symmetry_vdw_other 0.19 r_nbtor_refined 0.182 r_nbtor_other 0.093 r_chiral_restr 0.092 r_xyhbond_nbd_other 0.075 r_bond_refined_d 0.017 r_bond_other_d 0.003 r_gen_planes_refined 0.003 r_gen_planes_other 0.001 r_metal_ion_refined 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 3478 Nucleic Acid Atoms Solvent Atoms 160 Heterogen Atoms 83
Software Software Software Name Purpose SCALA data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction MOSFLM data reduction