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Structure of S2-198 TCR in complex with HLA-A*03:01 bound to ELFSYLIEK peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5BRZ experimental model PDB 5XOT experimental model PDB 3RL1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 50 mM MOPS pH 6.7, 14 % w/v PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.58 52.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.133 α = 90 b = 48.854 β = 92.84 c = 124.21 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 X 16M 2021-05-14 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) 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 2.05 68.82 99.43 0.107 0.115 0.043 0.998 12.3 6.9 60565
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 2.05 2.09 97.55 1.131 1.222 0.46 0.705 0.9 6.9
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 (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 THROUGHOUT 2.05 68.82 57579 2973 99.4 0.2207 0.21945 0.2269 0.2445 0.2504 RANDOM 46.406
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] 1.24 -0.02 -2.35 1.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.477 r_dihedral_angle_4_deg 14.488 r_dihedral_angle_3_deg 12.927 r_dihedral_angle_1_deg 6.563 r_long_range_B_refined 4.235 r_long_range_B_other 4.192 r_scangle_other 1.475 r_mcangle_it 1.444 r_mcangle_other 1.444 r_angle_refined_deg 1.183
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.477 r_dihedral_angle_4_deg 14.488 r_dihedral_angle_3_deg 12.927 r_dihedral_angle_1_deg 6.563 r_long_range_B_refined 4.235 r_long_range_B_other 4.192 r_scangle_other 1.475 r_mcangle_it 1.444 r_mcangle_other 1.444 r_angle_refined_deg 1.183 r_angle_other_deg 1.075 r_scbond_it 0.896 r_scbond_other 0.885 r_mcbond_it 0.839 r_mcbond_other 0.839 r_chiral_restr 0.037 r_bond_refined_d 0.003 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6478 Nucleic Acid Atoms Solvent Atoms 249 Heterogen Atoms 24
Software Software Software Name Purpose REFMAC refinement DIALS data reduction DIALS data scaling PHASER phasing