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Crystal structure of high affinity TCR in complex with pHLA harbouring bacterial peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6GH1 6GH1, 4WW2 experimental model PDB 4WW2 6GH1, 4WW2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 293 0.2 M calcium acetate, 0.1 M imidazole pH 8.0, 10% PEG 8000
Crystal Properties Matthews coefficient Solvent content 3.57 65.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 326.828 α = 90 b = 79.879 β = 96.894 c = 104.073 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 EIGER2 X 16M 2020-09-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 2.33 82.9 100 0.121 0.131 0.987 11.3 6.8 114168
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.33 2.37 100 3.209 3.521 0.34 6
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 6GH1, 4WW2 2.33 82.9 114144 5685 99.947 0.245 0.2425 0.2886 0.2478 74.978
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] -2.741 -2.502 6.869 -3.423
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.324 r_dihedral_angle_4_deg 20.089 r_dihedral_angle_3_deg 17.572 r_lrange_it 12.213 r_lrange_other 12.213 r_mcangle_it 8.545 r_mcangle_other 8.544 r_scangle_it 8.322 r_scangle_other 8.322 r_dihedral_angle_1_deg 7.377
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.324 r_dihedral_angle_4_deg 20.089 r_dihedral_angle_3_deg 17.572 r_lrange_it 12.213 r_lrange_other 12.213 r_mcangle_it 8.545 r_mcangle_other 8.544 r_scangle_it 8.322 r_scangle_other 8.322 r_dihedral_angle_1_deg 7.377 r_mcbond_other 5.65 r_mcbond_it 5.649 r_scbond_it 5.272 r_scbond_other 5.271 r_angle_refined_deg 1.406 r_angle_other_deg 1.153 r_symmetry_nbd_refined 0.286 r_nbd_other 0.264 r_symmetry_xyhbond_nbd_refined 0.208 r_nbd_refined 0.199 r_symmetry_nbd_other 0.191 r_xyhbond_nbd_refined 0.179 r_nbtor_refined 0.164 r_symmetry_xyhbond_nbd_other 0.134 r_ncsr_local_group_3 0.091 r_ncsr_local_group_1 0.082 r_symmetry_nbtor_other 0.076 r_ncsr_local_group_4 0.066 r_chiral_restr 0.053 r_ncsr_local_group_2 0.035 r_bond_refined_d 0.006 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12837 Nucleic Acid Atoms Solvent Atoms 281 Heterogen Atoms 8
Software Software Software Name Purpose REFMAC refinement DIALS data reduction DIALS data scaling PHASER phasing