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Directed Evolution of Human T-cell Receptor CDR2 residues by phage display dramatically enhances affinity for cognate peptide-MHC without apparent cross-reactivity
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2BNR PDB ENTRY 2BNR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 85 mM HEPES, 8.5% Iso-propanol, 17% PEG4000, 15% glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.62 53.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.234 α = 90 b = 53.972 β = 96.83 c = 119.905 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 2004-05-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SRS BEAMLINE PX14.1 1.488 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 37.85 98.7 0.178 0.178 3 10.4 64982 28.5
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 2.11 97.4 0.011 0.01072 0.5 9.1 9272
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 (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT R-free PDB ENTRY 2BNR 2.1 37.85 56251 2910 98.695 0.169 0.169 0.166 0.2311 0.2934 Random 14.392
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] 0.072 -0.327 0.847 -0.997
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 20.481 r_scangle_it 9.98 r_dihedral_angle_4_deg 8.841 r_dihedral_angle_3_deg 8.503 r_scbond_it 7.102 r_scangle_other 4.955 r_mcangle_it 4.81 r_mcbond_it 3.293 r_mcangle_other 2.363 r_scbond_other 2.232
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 20.481 r_scangle_it 9.98 r_dihedral_angle_4_deg 8.841 r_dihedral_angle_3_deg 8.503 r_scbond_it 7.102 r_scangle_other 4.955 r_mcangle_it 4.81 r_mcbond_it 3.293 r_mcangle_other 2.363 r_scbond_other 2.232 r_dihedral_angle_1_deg 1.904 r_angle_refined_deg 1.536 r_angle_other_deg 1.284 r_mcbond_other 1.158 r_symmetry_hbond_refined 0.33 r_metal_ion_refined 0.236 r_symmetry_vdw_other 0.232 r_xyhbond_nbd_refined 0.227 r_symmetry_vdw_refined 0.224 r_nbd_refined 0.212 r_nbd_other 0.203 r_nbtor_refined 0.188 r_xyhbond_nbd_other 0.133 r_chiral_restr 0.115 r_nbtor_other 0.09 r_bond_refined_d 0.014 r_gen_planes_refined 0.014 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6562 Nucleic Acid Atoms Solvent Atoms 728 Heterogen Atoms 25
Software Software Software Name Purpose SCALA data scaling AMoRE phasing REFMAC refinement PDB_EXTRACT data extraction MOSFLM data reduction CCP4 data scaling