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Structure of S2 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 HEPES pH 7.0, 13 % w/v PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.63 53.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.66 α = 90 b = 49.2 β = 92.93 c = 124.67 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 PILATUS 6M-F 2017-11-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.9159 Diamond I04-1
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 2.34 41.5 99.85 0.078 0.084 0.031 0.999 14.3 7.2 41755
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 2.34 2.38 99.9 1.201 1.317 0.53 0.537 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 (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 2.34 41.5 39600 2145 99.8 0.24422 0.24273 0.2519 0.27213 0.277 RANDOM 68.73
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] -1.85 -2.64 3.11 -0.99
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.958 r_dihedral_angle_3_deg 12.732 r_dihedral_angle_4_deg 10.194 r_dihedral_angle_1_deg 5.557 r_long_range_B_refined 2.432 r_long_range_B_other 2.431 r_angle_refined_deg 1.161 r_angle_other_deg 1.022 r_mcangle_it 0.706 r_mcangle_other 0.706
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.958 r_dihedral_angle_3_deg 12.732 r_dihedral_angle_4_deg 10.194 r_dihedral_angle_1_deg 5.557 r_long_range_B_refined 2.432 r_long_range_B_other 2.431 r_angle_refined_deg 1.161 r_angle_other_deg 1.022 r_mcangle_it 0.706 r_mcangle_other 0.706 r_scangle_other 0.569 r_mcbond_it 0.386 r_mcbond_other 0.386 r_scbond_it 0.322 r_scbond_other 0.322 r_chiral_restr 0.03 r_bond_refined_d 0.002 r_gen_planes_refined 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 6370 Nucleic Acid Atoms Solvent Atoms 60 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling PHASER phasing