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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 PACT Premier E04: 0.2 M K SCN, 20% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.5 50.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.35 α = 90 b = 114.81 β = 90 c = 50.73 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 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 1.6 50.73 99.7 0.046 0.05 0.999 19.8 6.6 65936
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 1.6 1.65 99.8 0.729 0.787 0.827 2.7 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 1.6 50.73 62540 3342 99.56 0.1746 0.17264 0.1834 0.21136 0.22 RANDOM 29.454
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] 0.11 0.54 -0.65
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.148 r_dihedral_angle_4_deg 15.238 r_dihedral_angle_3_deg 14.089 r_dihedral_angle_1_deg 7.054 r_long_range_B_refined 6.541 r_long_range_B_other 6.541 r_scangle_other 2.5 r_mcangle_it 1.956 r_mcangle_other 1.955 r_angle_refined_deg 1.862
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.148 r_dihedral_angle_4_deg 15.238 r_dihedral_angle_3_deg 14.089 r_dihedral_angle_1_deg 7.054 r_long_range_B_refined 6.541 r_long_range_B_other 6.541 r_scangle_other 2.5 r_mcangle_it 1.956 r_mcangle_other 1.955 r_angle_refined_deg 1.862 r_scbond_it 1.718 r_scbond_other 1.702 r_mcbond_it 1.181 r_mcbond_other 1.181 r_angle_other_deg 1.026 r_chiral_restr 0.113 r_bond_refined_d 0.016 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 3495 Nucleic Acid Atoms Solvent Atoms 380 Heterogen Atoms 131
Software Software Software Name Purpose REFMAC refinement xia2 data reduction XDS data reduction Aimless data scaling PHASER phasing