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Crystal structure of ELS4 TCR bound to HLA-B*3501 presenting EBV peptide EPLPQGQLTAY at 1.7A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ZSD 1ZSD, 2NW2 experimental model PDB 2NW2 1ZSD, 2NW2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.4 277 0.1M Na Cacodylate (pH6.4), 0.2M CaCl2, 16% PEG 3350, 3% 1,6Hexanediol, vapor diffusion, hanging drop, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.45 49.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 118.479 α = 90 b = 118.067 β = 96.04 c = 131.465 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 2005-11-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID APS 17-ID
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 2.7 87783
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-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1ZSD, 2NW2 2.7 30 87783 4598 93.52 0.27169 0.26876 0.32702 RANDOM 44.267
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] 0.76 0.17 1.64 -2.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.788 r_dihedral_angle_3_deg 16.581 r_dihedral_angle_4_deg 15.895 r_dihedral_angle_1_deg 5.246 r_scangle_it 2.731 r_scbond_it 1.806 r_mcangle_it 1.5 r_angle_refined_deg 0.959 r_mcbond_it 0.829 r_nbtor_refined 0.299
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.788 r_dihedral_angle_3_deg 16.581 r_dihedral_angle_4_deg 15.895 r_dihedral_angle_1_deg 5.246 r_scangle_it 2.731 r_scbond_it 1.806 r_mcangle_it 1.5 r_angle_refined_deg 0.959 r_mcbond_it 0.829 r_nbtor_refined 0.299 r_symmetry_vdw_refined 0.204 r_nbd_refined 0.188 r_symmetry_hbond_refined 0.16 r_xyhbond_nbd_refined 0.137 r_chiral_restr 0.066 r_bond_refined_d 0.006 r_gen_planes_refined 0.002 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 26287 Nucleic Acid Atoms Solvent Atoms 194 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction