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TCR in complex with HLA-E*01:03 bound to HBV envelope 371-379 index 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 3.04 59.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.698 α = 90 b = 155.061 β = 97.043 c = 93.414 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 2.25 79.57 98.6 0.15 0.06 0.998 10.5 7.2 104999
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 2.25 2.29 2.958 1.164 0.493
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.25 79.57 104896 5132 98.48 0.211 0.2094 0.2521 0.2158 RANDOM 66.902
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] 0.414 2.591 2.06 -3.022
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.618 r_dihedral_angle_3_deg 15.902 r_lrange_other 11.499 r_lrange_it 11.497 r_dihedral_angle_2_deg 10.497 r_scangle_it 8.776 r_scangle_other 8.775 r_mcangle_it 8.1 r_mcangle_other 8.1 r_dihedral_angle_1_deg 7.833
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.618 r_dihedral_angle_3_deg 15.902 r_lrange_other 11.499 r_lrange_it 11.497 r_dihedral_angle_2_deg 10.497 r_scangle_it 8.776 r_scangle_other 8.775 r_mcangle_it 8.1 r_mcangle_other 8.1 r_dihedral_angle_1_deg 7.833 r_scbond_it 5.857 r_scbond_other 5.853 r_mcbond_it 5.523 r_mcbond_other 5.522 r_angle_refined_deg 1.57 r_angle_other_deg 0.545 r_symmetry_xyhbond_nbd_refined 0.288 r_nbd_refined 0.212 r_symmetry_nbd_other 0.199 r_nbtor_refined 0.182 r_nbd_other 0.164 r_xyhbond_nbd_refined 0.161 r_symmetry_nbd_refined 0.142 r_ncsr_local_group_3 0.114 r_ncsr_local_group_4 0.113 r_ncsr_local_group_1 0.088 r_symmetry_nbtor_other 0.086 r_ncsr_local_group_2 0.083 r_chiral_restr 0.069 r_symmetry_xyhbond_nbd_other 0.031 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 12808 Nucleic Acid Atoms Solvent Atoms 246 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement DIALS data reduction DIALS data scaling PHASER phasing