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Structure of S8 TCR in complex with HLA-A*03:01 bound to ELFSYLIEK peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5BRZ experimental model PDB 3RL1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 50 mM Magnesium acetate, 20 mM MOPS pH 7.2, 50 mM Sodium chloride, 12 % w/v PEG 8000
Crystal Properties Matthews coefficient Solvent content 3.06 59.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 208.12 α = 90 b = 45.71 β = 94.93 c = 121.68 γ = 90
Symmetry Space Group C 1 2 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 2018-08-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.9159 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.81 121.23 99.93 0.061 0.066 0.024 0.999 14.6 7.2 104807
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.81 1.84 99.98 1.182 1.297 0.526 0.604 1.2 6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.81 121.23 99734 5073 99.93 0.22186 0.22088 0.2284 0.24099 0.2483 RANDOM 53.154
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] -0.44 -1.31 1.87 -1.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.369 r_dihedral_angle_4_deg 15.591 r_dihedral_angle_3_deg 11.961 r_long_range_B_refined 6.312 r_long_range_B_other 6.288 r_dihedral_angle_1_deg 6.265 r_scangle_other 1.466 r_mcangle_it 1.238 r_mcangle_other 1.238 r_angle_refined_deg 1.168
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.369 r_dihedral_angle_4_deg 15.591 r_dihedral_angle_3_deg 11.961 r_long_range_B_refined 6.312 r_long_range_B_other 6.288 r_dihedral_angle_1_deg 6.265 r_scangle_other 1.466 r_mcangle_it 1.238 r_mcangle_other 1.238 r_angle_refined_deg 1.168 r_angle_other_deg 1.083 r_scbond_it 0.924 r_scbond_other 0.924 r_mcbond_it 0.716 r_mcbond_other 0.715 r_chiral_restr 0.038 r_gen_planes_refined 0.003 r_bond_refined_d 0.002 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 6498 Nucleic Acid Atoms Solvent Atoms 354 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling PHASER phasing