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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 291 0.2M Na Malonate, 20% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.5 50.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.08 α = 90 b = 115.3 β = 90 c = 50.65 γ = 90
Symmetry Space Group P 21 21 2
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 1.58 46.37 99 0.041 0.045 0.999 23.6 6.6 69019
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 1.58 1.62 100 0.654 0.707 0.841 3.1 7
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 1.58 46.37 65474 3488 99.88 0.17542 0.17375 0.1841 0.20743 0.2186 RANDOM 26.652
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] 0.06 0.3 -0.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.111 r_dihedral_angle_3_deg 14.071 r_dihedral_angle_4_deg 12.985 r_dihedral_angle_1_deg 7.703 r_long_range_B_refined 6.87 r_long_range_B_other 6.87 r_scangle_other 2.424 r_angle_refined_deg 1.904 r_mcangle_it 1.796 r_mcangle_other 1.796
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.111 r_dihedral_angle_3_deg 14.071 r_dihedral_angle_4_deg 12.985 r_dihedral_angle_1_deg 7.703 r_long_range_B_refined 6.87 r_long_range_B_other 6.87 r_scangle_other 2.424 r_angle_refined_deg 1.904 r_mcangle_it 1.796 r_mcangle_other 1.796 r_scbond_it 1.638 r_scbond_other 1.637 r_mcbond_it 1.112 r_mcbond_other 1.109 r_angle_other_deg 1.058 r_chiral_restr 0.122 r_bond_refined_d 0.017 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 3493 Nucleic Acid Atoms Solvent Atoms 389 Heterogen Atoms 68
Software Software Software Name Purpose REFMAC refinement xia2 data reduction XDS data reduction Aimless data scaling PHASER phasing