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HA1.7 Human T-Cell Receptor specific for Influenza virus epitope PKYVKQNTLKLAT presented by Human Leukocyte Antigen HLA-DR0101
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4GKZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 15% PEG 4K, 15% Glycerol, 100mM MES pH 7.0
Crystal Properties Matthews coefficient Solvent content 2.53 51.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.46 α = 90 b = 49.96 β = 93.08 c = 72.75 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 2012-02-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.9173 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.49 48.87 98.5 17.5 3.7 17434 64.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.49 2.55 99.2 0.52 0.703 0.353 2.3 3.9 1273
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 4GKZ 2.49 48.87 16545 881 98.25 0.23539 0.23225 0.2328 0.29651 0.2907 RANDOM 65.654
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] -0.31 -0.58 1.81 -1.46
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.79 r_dihedral_angle_4_deg 22.064 r_dihedral_angle_3_deg 20.986 r_dihedral_angle_1_deg 7.545 r_long_range_B_refined 2.899 r_long_range_B_other 2.899 r_angle_refined_deg 1.645 r_mcangle_it 1.071 r_mcangle_other 1.071 r_angle_other_deg 0.86
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.79 r_dihedral_angle_4_deg 22.064 r_dihedral_angle_3_deg 20.986 r_dihedral_angle_1_deg 7.545 r_long_range_B_refined 2.899 r_long_range_B_other 2.899 r_angle_refined_deg 1.645 r_mcangle_it 1.071 r_mcangle_other 1.071 r_angle_other_deg 0.86 r_mcbond_it 0.652 r_mcbond_other 0.652 r_scangle_other 0.644 r_scbond_it 0.41 r_scbond_other 0.41 r_chiral_restr 0.098 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 3505 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement xia2 data reduction XDS data reduction SCALA data scaling PHASER phasing