☰ Navigation Tabs
TCR in complex with HLA-E*01:03 bound to HBV envelope 371-379 L6I 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
Collection Temp: 100
Crystal Properties Matthews coefficient Solvent content 3.04 59.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.185 α = 90 b = 153.813 β = 96.628 c = 93.4 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 2.609 79.65 99.2 0.142 0.057 0.998 0.142 7.1 67783
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 2.609 2.65 3.246 1.345 0.313 0.4
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 2.609 79.65 67726 3360 99.097 0.2 0.1976 0.2088 0.2506 0.2613 94.35
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] 0.208 4.013 2.416 -3.464
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.556 r_dihedral_angle_6_deg 16.024 r_lrange_it 15.958 r_lrange_other 15.957 r_scangle_it 12.673 r_scangle_other 12.672 r_mcangle_it 12.59 r_mcangle_other 12.589 r_dihedral_angle_2_deg 11.812 r_mcbond_it 8.698
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.556 r_dihedral_angle_6_deg 16.024 r_lrange_it 15.958 r_lrange_other 15.957 r_scangle_it 12.673 r_scangle_other 12.672 r_mcangle_it 12.59 r_mcangle_other 12.589 r_dihedral_angle_2_deg 11.812 r_mcbond_it 8.698 r_mcbond_other 8.688 r_scbond_it 8.564 r_scbond_other 8.563 r_dihedral_angle_1_deg 8.43 r_angle_refined_deg 1.625 r_angle_other_deg 0.547 r_symmetry_xyhbond_nbd_refined 0.217 r_nbd_refined 0.21 r_symmetry_nbd_other 0.205 r_nbd_other 0.189 r_nbtor_refined 0.184 r_xyhbond_nbd_refined 0.152 r_ncsr_local_group_4 0.123 r_ncsr_local_group_3 0.113 r_symmetry_nbd_refined 0.105 r_ncsr_local_group_2 0.093 r_ncsr_local_group_1 0.091 r_symmetry_nbtor_other 0.087 r_chiral_restr 0.067 r_symmetry_xyhbond_nbd_other 0.02 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12910 Nucleic Acid Atoms Solvent Atoms 130 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement DIALS data reduction DIALS data scaling PHASER phasing