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F11 T-Cell Receptor Recognising PKYVKQNTLKLAT Peptide Presented by HLA-DR*0101
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6EH6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 291 0.2 M NH4 SO4, 0.1 M MES, 25% PEG 4K
Crystal Properties Matthews coefficient Solvent content 2.5 50.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.65 α = 90 b = 114.86 β = 91.01 c = 85.33 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 PIXEL DECTRIS PILATUS3 S 6M 2012-10-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.9200 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) 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 1.73 46.34 94.8 0.074 0.088 0.996 11.1 3.3 96229
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.73 1.77 98.6 0.656 0.777 0.663 2 3.5
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 6EH6 1.73 46.34 91379 4819 94.75 0.19101 0.18921 0.1969 0.22563 0.2337 RANDOM 26.356
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] -0.45 -0.27 -0.5 0.96
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.183 r_dihedral_angle_3_deg 14.581 r_dihedral_angle_4_deg 11.885 r_dihedral_angle_1_deg 7.559 r_long_range_B_other 6.779 r_long_range_B_refined 6.778 r_scangle_other 2.328 r_angle_refined_deg 1.901 r_mcangle_other 1.847 r_mcangle_it 1.846
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.183 r_dihedral_angle_3_deg 14.581 r_dihedral_angle_4_deg 11.885 r_dihedral_angle_1_deg 7.559 r_long_range_B_other 6.779 r_long_range_B_refined 6.778 r_scangle_other 2.328 r_angle_refined_deg 1.901 r_mcangle_other 1.847 r_mcangle_it 1.846 r_scbond_it 1.541 r_scbond_other 1.534 r_mcbond_it 1.125 r_mcbond_other 1.125 r_angle_other_deg 1.059 r_chiral_restr 0.124 r_bond_refined_d 0.018 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6990 Nucleic Acid Atoms Solvent Atoms 637 Heterogen Atoms 173
Software Software Software Name Purpose REFMAC refinement xia2 data reduction XDS data reduction Aimless data scaling PHASER phasing