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Structure of S8-9F3 TCR in complex with HLA-A*11:01 bound to ELFSYLIEK peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5BRZ experimental model PDB 1Q94
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 150 mM Magnesium acetate, 20 mM MOPS pH 7.2, 12 % w/v PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.59 52.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.02 α = 90.9 b = 88.89 β = 98.54 c = 121.86 γ = 97.72
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 2020-12-10 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 2.49 45.07 98.43 0.077 0.089 0.044 0.998 9.3 4 65184
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 2.49 2.53 97.9 1.734 2 0.987 0.279 0.7 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 (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 2.49 45.07 62015 3169 98.42 0.24651 0.2447 0.2493 0.28286 0.2853 RANDOM 80.397
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] 3.41 -3.9 1.48 1.77 -0.21 -4.4
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.165 r_dihedral_angle_3_deg 15.848 r_dihedral_angle_4_deg 12.77 r_dihedral_angle_1_deg 6.224 r_long_range_B_refined 1.698 r_long_range_B_other 1.698 r_angle_refined_deg 1.197 r_angle_other_deg 1.042 r_mcangle_it 0.929 r_mcangle_other 0.929
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.165 r_dihedral_angle_3_deg 15.848 r_dihedral_angle_4_deg 12.77 r_dihedral_angle_1_deg 6.224 r_long_range_B_refined 1.698 r_long_range_B_other 1.698 r_angle_refined_deg 1.197 r_angle_other_deg 1.042 r_mcangle_it 0.929 r_mcangle_other 0.929 r_scangle_other 0.693 r_mcbond_other 0.51 r_mcbond_it 0.509 r_scbond_it 0.374 r_scbond_other 0.374 r_chiral_restr 0.034 r_gen_planes_refined 0.003 r_bond_refined_d 0.002 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 12978 Nucleic Acid Atoms Solvent Atoms 22 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling PHASER phasing