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Crystal structure of the T-cell receptor NYE_S3 bound to HLA A2*01-SLLMWITQV
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5E00 5e00 (chains A and B), 3QDJ (chain D) and 5D2N (chain E) experimental model PDB 3QDJ 5e00 (chains A and B), 3QDJ (chain D) and 5D2N (chain E) experimental model PDB 5D2N 5e00 (chains A and B), 3QDJ (chain D) and 5D2N (chain E)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.2 M ammonium sulphate, 15 % PEG8k, 0.1 M Tris pH7.5
Crystal Properties Matthews coefficient Solvent content 3.25 62.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 106.57 α = 90 b = 85.61 β = 91.78 c = 171.92 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 PILATUS 6M-F 2017-09-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.91587 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim 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 3.12 85.61 100 0.117 0.047 0.999 10.99 6.76 52792
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.12 3.2 100 0.999 0.567 0.627 1.25 3.97
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 5e00 (chains A and B), 3QDJ (chain D) and 5D2N (chain E) 3.12 68.01 52792 2717 99.94 0.22481 0.22349 0.225 0.25046 0.252 RANDOM 117.682
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] -3.55 -2.27 -1.37 5.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.057 r_dihedral_angle_3_deg 12.213 r_dihedral_angle_4_deg 9.839 r_dihedral_angle_1_deg 4.953 r_long_range_B_refined 1.859 r_long_range_B_other 1.859 r_mcangle_it 1.166 r_mcangle_other 1.166 r_angle_refined_deg 0.929 r_angle_other_deg 0.796
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.057 r_dihedral_angle_3_deg 12.213 r_dihedral_angle_4_deg 9.839 r_dihedral_angle_1_deg 4.953 r_long_range_B_refined 1.859 r_long_range_B_other 1.859 r_mcangle_it 1.166 r_mcangle_other 1.166 r_angle_refined_deg 0.929 r_angle_other_deg 0.796 r_scangle_other 0.792 r_mcbond_it 0.629 r_mcbond_other 0.629 r_scbond_it 0.418 r_scbond_other 0.418 r_chiral_restr 0.06 r_bond_refined_d 0.006 r_gen_planes_refined 0.003 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 16633 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling PHASER phasing