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Crystal structure of engineered TCR (756) 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 7PBC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 293.15 0.2M Sodium chloride, 0.1M MES pH 6.0, 20% w/v PEG 6000
Crystal Properties Matthews coefficient Solvent content 2.52 51.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.197 α = 90 b = 77.446 β = 102.7 c = 116.682 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 1.54 77.45 96.9 0.075 0.105 0.073 0.995 6.4 3.2 134415 18.43
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 1.54 1.57 95.8 0.984 1.381 0.967 0.331 1 3.1
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-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 7PBC 1.54 64.113 134385 6619 96.664 0.204 0.2019 0.2032 0.2364 0.239 25.417
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] -0.768 0.149 -0.793 1.356
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.142 r_dihedral_angle_4_deg 14.894 r_dihedral_angle_3_deg 13.894 r_dihedral_angle_1_deg 7.53 r_lrange_it 6.306 r_lrange_other 6.305 r_scangle_it 4.561 r_scangle_other 4.56 r_mcangle_it 3.556 r_mcangle_other 3.555
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.142 r_dihedral_angle_4_deg 14.894 r_dihedral_angle_3_deg 13.894 r_dihedral_angle_1_deg 7.53 r_lrange_it 6.306 r_lrange_other 6.305 r_scangle_it 4.561 r_scangle_other 4.56 r_mcangle_it 3.556 r_mcangle_other 3.555 r_scbond_it 2.983 r_scbond_other 2.983 r_mcbond_it 2.341 r_mcbond_other 2.34 r_angle_refined_deg 1.631 r_angle_other_deg 1.38 r_xyhbond_nbd_refined 0.211 r_symmetry_nbd_refined 0.2 r_nbd_refined 0.198 r_symmetry_nbd_other 0.193 r_nbd_other 0.188 r_symmetry_xyhbond_nbd_other 0.179 r_symmetry_xyhbond_nbd_refined 0.174 r_nbtor_refined 0.168 r_symmetry_nbtor_other 0.08 r_chiral_restr 0.078 r_bond_refined_d 0.01 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6470 Nucleic Acid Atoms Solvent Atoms 528 Heterogen Atoms 24
Software Software Software Name Purpose REFMAC refinement REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing Coot model building