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Crystal Structure of the LC13 TCR in complex with HLA B*4405 bound to EEYLKAWTF a mimotope
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1SYV PDB entries 1SYV and 1KGC experimental model PDB 1KGC PDB entries 1SYV and 1KGC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 277 0.2M NaOAc, 12-18% PEG 4000, 0.1M Tris, pH 8.5, vapor diffusion, hanging drop, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.2 44.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 223.117 α = 90 b = 53.217 β = 102.39 c = 143.202 γ = 90
Symmetry Space Group C 1 2 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 210r 2008-11-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX1 1 Australian Synchrotron MX1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.6 50 97.8 0.112 6.8 3.2 50197
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.6 2.69 97.8 0.453 3 4976
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 PDB entries 1SYV and 1KGC 2.6 50 50191 2538 97.53 0.222 0.219 0.2546 0.279 0.3003 RANDOM 36.4
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] 1.5 1.74 -1.7 0.95
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.61 r_dihedral_angle_3_deg 15.009 r_dihedral_angle_4_deg 13.084 r_dihedral_angle_1_deg 5.75 r_scangle_it 2.366 r_scbond_it 1.516 r_mcangle_it 1.033 r_angle_refined_deg 0.926 r_mcbond_it 0.591 r_nbtor_refined 0.295
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.61 r_dihedral_angle_3_deg 15.009 r_dihedral_angle_4_deg 13.084 r_dihedral_angle_1_deg 5.75 r_scangle_it 2.366 r_scbond_it 1.516 r_mcangle_it 1.033 r_angle_refined_deg 0.926 r_mcbond_it 0.591 r_nbtor_refined 0.295 r_nbd_refined 0.168 r_symmetry_vdw_refined 0.167 r_symmetry_hbond_refined 0.129 r_xyhbond_nbd_refined 0.111 r_chiral_restr 0.062 r_bond_refined_d 0.006 r_gen_planes_refined 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13318 Nucleic Acid Atoms Solvent Atoms 116 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction