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Crystal Structures of High Affinity Human T-Cell Receptors Bound to pMHC RevealNative Diagonal Binding Geometry TCR Clone C5C1 Complexed with MHC
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 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 2.51 51.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.752 α = 90 b = 52.907 β = 97.94 c = 119.904 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 PX14.2 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 2.3 118.68 91.3 0.151 0.151 4.4 2.9 38083
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 2.3 2.42 84.6 0.794 0.052 1.3 2.8 1337
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 2.3 118.68 36136 1918 0.19642 0.19172 0.1955 0.28333 0.2825 RANDOM 16.258
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] 0.14 2.21 1.4 -0.93
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 20.749 r_scangle_it 8.987 r_dihedral_angle_3_deg 7.78 r_scbond_it 6.937 r_dihedral_angle_4_deg 5.942 r_mcangle_it 4.843 r_mcbond_it 3.443 r_dihedral_angle_1_deg 1.632 r_angle_refined_deg 1.497 r_mcbond_other 0.985
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 20.749 r_scangle_it 8.987 r_dihedral_angle_3_deg 7.78 r_scbond_it 6.937 r_dihedral_angle_4_deg 5.942 r_mcangle_it 4.843 r_mcbond_it 3.443 r_dihedral_angle_1_deg 1.632 r_angle_refined_deg 1.497 r_mcbond_other 0.985 r_angle_other_deg 0.88 r_symmetry_hbond_refined 0.202 r_xyhbond_nbd_refined 0.197 r_symmetry_vdw_other 0.191 r_nbd_other 0.184 r_nbtor_refined 0.177 r_nbd_refined 0.174 r_symmetry_vdw_refined 0.166 r_chiral_restr 0.09 r_nbtor_other 0.085 r_xyhbond_nbd_other 0.056 r_bond_refined_d 0.012 r_gen_planes_refined 0.004 r_bond_other_d 0.002 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 6566 Nucleic Acid Atoms Solvent Atoms 394 Heterogen Atoms 162
Software Software Software Name Purpose SCALA data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction MOSFLM data reduction