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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 6.5 291 0.2M NaF, 0.1M Bis-Tris Propane, 20% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.5 50.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.28 α = 90 b = 114.81 β = 90 c = 50.7 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 1.59 46.38 99.7 0.043 0.047 1 22.7 6.6 67125
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 1.59 1.63 100 0.72 0.779 0.824 2.9 6.9
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 1.59 46.38 63670 3398 99.66 0.1756 0.17441 0.1846 0.19751 0.2081 RANDOM 27.174
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] 0.3 0.2 -0.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.537 r_dihedral_angle_4_deg 14.036 r_dihedral_angle_3_deg 13.722 r_dihedral_angle_1_deg 7.176 r_long_range_B_refined 6.395 r_long_range_B_other 6.317 r_scangle_other 2.602 r_angle_refined_deg 1.952 r_mcangle_it 1.884 r_mcangle_other 1.884
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.537 r_dihedral_angle_4_deg 14.036 r_dihedral_angle_3_deg 13.722 r_dihedral_angle_1_deg 7.176 r_long_range_B_refined 6.395 r_long_range_B_other 6.317 r_scangle_other 2.602 r_angle_refined_deg 1.952 r_mcangle_it 1.884 r_mcangle_other 1.884 r_scbond_it 1.785 r_scbond_other 1.776 r_mcbond_it 1.173 r_mcbond_other 1.173 r_angle_other_deg 1.077 r_chiral_restr 0.123 r_bond_refined_d 0.018 r_gen_planes_refined 0.01 r_bond_other_d 0.003 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 338 Heterogen Atoms 98
Software Software Software Name Purpose REFMAC refinement XDS data reduction xia2 data reduction Aimless data scaling PHASER phasing