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Crystal structure of engineered TCR (796) complexed to HLA-A*02:01 presenting MAGE-A10 9-mer peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3QEU 3QEU, 1I4F experimental model PDB 1I4F 3QEU, 1I4F
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293.15 0.2M Sodium bromide, 0.1M Bis-Tris propane pH 8.5, 20% w/v PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.4903 50.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.33 α = 90 b = 77.5 β = 102.88 c = 115.12 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 6M 2018-05-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97625 Diamond I03
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 2.04 77.5 99.4 0.105 0.145 0.1 0.988 5.7 2.9 59081
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 2.04 2.09 0.736 1.005 0.681 0.728 2.8
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 (All) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3QEU, 1I4F 2.04 63.853 59058 2817 99.287 0.189 0.1865 0.2361 0.2436 Random 34.492
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] -2.622 -0.639 0.64 2.059
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.117 r_dihedral_angle_3_deg 15.261 r_dihedral_angle_4_deg 13.698 r_dihedral_angle_1_deg 7.596 r_lrange_it 6.608 r_lrange_other 6.59 r_scangle_it 4.689 r_scangle_other 4.689 r_mcangle_it 3.94 r_mcangle_other 3.94
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.117 r_dihedral_angle_3_deg 15.261 r_dihedral_angle_4_deg 13.698 r_dihedral_angle_1_deg 7.596 r_lrange_it 6.608 r_lrange_other 6.59 r_scangle_it 4.689 r_scangle_other 4.689 r_mcangle_it 3.94 r_mcangle_other 3.94 r_scbond_it 3.035 r_scbond_other 3.035 r_mcbond_other 2.56 r_mcbond_it 2.559 r_angle_refined_deg 1.491 r_angle_other_deg 1.264 r_xyhbond_nbd_refined 0.305 r_symmetry_xyhbond_nbd_refined 0.258 r_nbd_refined 0.195 r_symmetry_nbd_other 0.188 r_symmetry_nbd_refined 0.182 r_nbtor_refined 0.165 r_nbd_other 0.154 r_symmetry_nbtor_other 0.077 r_chiral_restr 0.063 r_symmetry_xyhbond_nbd_other 0.029 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6452 Nucleic Acid Atoms Solvent Atoms 346 Heterogen Atoms 19
Software Software Software Name Purpose REFMAC refinement REFMAC refinement Aimless data scaling MOSFLM data reduction Coot model building PHASER phasing