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TCR in complex with HLA-E*01:03 bound to HBV envelope 371-379 S3N peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7NDQ experimental model PDB 5MEN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 20% (w/v) PEG 3350, 100 mM BIS-TRIS propane pH 8.5, 200 mM sodium sulfate
Crystal Properties Matthews coefficient Solvent content 2.9 57.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.417 α = 90 b = 147.845 β = 99.026 c = 91.908 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 EIGER2 XE 16M 2022-02-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.97950 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.35 65.51 99.4 0.159 0.065 0.992 9.3 6.9 88665
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.35 2.39 1.606 0.758 0.521 0.6
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.35 65.51 88609 4288 99.293 0.211 0.2083 0.2143 0.2609 0.2675 58.715
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] -0.466 2.556 0.914 -1.199
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.764 r_dihedral_angle_6_deg 16.225 r_dihedral_angle_2_deg 12.598 r_lrange_it 12.419 r_lrange_other 12.419 r_scangle_it 9.938 r_scangle_other 9.937 r_mcangle_other 8.962 r_mcangle_it 8.959 r_dihedral_angle_1_deg 7.762
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.764 r_dihedral_angle_6_deg 16.225 r_dihedral_angle_2_deg 12.598 r_lrange_it 12.419 r_lrange_other 12.419 r_scangle_it 9.938 r_scangle_other 9.937 r_mcangle_other 8.962 r_mcangle_it 8.959 r_dihedral_angle_1_deg 7.762 r_scbond_it 6.753 r_scbond_other 6.752 r_mcbond_it 6.276 r_mcbond_other 6.276 r_angle_refined_deg 1.567 r_angle_other_deg 0.529 r_symmetry_xyhbond_nbd_refined 0.293 r_nbd_refined 0.22 r_symmetry_nbd_other 0.208 r_symmetry_nbd_refined 0.197 r_nbd_other 0.187 r_nbtor_refined 0.186 r_xyhbond_nbd_refined 0.174 r_ncsr_local_group_4 0.14 r_ncsr_local_group_3 0.131 r_ncsr_local_group_1 0.102 r_ncsr_local_group_2 0.096 r_symmetry_nbtor_other 0.089 r_symmetry_xyhbond_nbd_other 0.072 r_chiral_restr 0.069 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12872 Nucleic Acid Atoms Solvent Atoms 237 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement DIALS data reduction DIALS data scaling PHASER phasing