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Crystal structure of parent TCR (728) 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 293.15 0.02M Sodium/potassium phosphate, 0.1M Bis-Tris propane pH 6.5, 20% w/v PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.6572 53.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.081 α = 109.17 b = 95.834 β = 96.51 c = 106.261 γ = 99.7
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 1.82 98.71 90.2 0.098 0.139 0.098 0.986 4.7 1.5 158062
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 1.82 1.85 0.672 0.95 0.672 0.464 0.7 1.4
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-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 FREE R-VALUE 7PBC 1.82 81.936 158060 8035 90.166 0.203 0.2028 0.2013 0.1942 0.2292 0.2201 Random selection 36.993
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] -2.023 0.947 0.098 2.143 0.857 -0.991
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.684 r_dihedral_angle_4_deg 14.923 r_dihedral_angle_3_deg 14.33 r_dihedral_angle_1_deg 7.622 r_lrange_it 7.273 r_lrange_other 7.265 r_scangle_it 5.245 r_scangle_other 5.238 r_mcangle_other 4.376 r_mcangle_it 4.375
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.684 r_dihedral_angle_4_deg 14.923 r_dihedral_angle_3_deg 14.33 r_dihedral_angle_1_deg 7.622 r_lrange_it 7.273 r_lrange_other 7.265 r_scangle_it 5.245 r_scangle_other 5.238 r_mcangle_other 4.376 r_mcangle_it 4.375 r_scbond_it 3.39 r_scbond_other 3.378 r_mcbond_it 2.912 r_mcbond_other 2.91 r_angle_refined_deg 1.471 r_angle_other_deg 1.277 r_nbd_refined 0.197 r_symmetry_nbd_other 0.184 r_nbd_other 0.184 r_xyhbond_nbd_refined 0.166 r_nbtor_refined 0.164 r_symmetry_nbd_refined 0.142 r_symmetry_xyhbond_nbd_refined 0.135 r_ncsr_local_group_4 0.091 r_ncsr_local_group_1 0.079 r_ncsr_local_group_2 0.078 r_symmetry_nbtor_other 0.077 r_symmetry_xyhbond_nbd_other 0.072 r_chiral_restr 0.067 r_ncsr_local_group_3 0.065 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13024 Nucleic Acid Atoms Solvent Atoms 644 Heterogen Atoms 17
Software Software Software Name Purpose REFMAC refinement REFMAC refinement MOSFLM data reduction Aimless data scaling PHASER phasing Coot model building