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Structure of E8 TCR in complex in human MR1 bound to 4FBA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5U6Q
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.1 M HEPES pH 7.5, 20% PEG 4000, 15% Glycerol
Crystal Properties Matthews coefficient Solvent content 2.55 51.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.54 α = 90 b = 96.24 β = 90 c = 117.25 γ = 90
Symmetry Space Group P 21 21 21
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 2019-11-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9763 Diamond I03
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 2.13 58.62 100 0.109 0.113 0.029 0.999 15.3 14.9 56786
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 2.13 2.17 100 2.656 2.746 0.692 0.468 1 15.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 5U6Q 2.13 58.62 53880 2838 99.98 0.19828 0.19586 0.2072 0.24367 0.2535 RANDOM 57.594
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] 3.13 -1.71 -1.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.062 r_dihedral_angle_4_deg 16.938 r_dihedral_angle_3_deg 16.081 r_dihedral_angle_1_deg 8.269 r_long_range_B_refined 8.034 r_long_range_B_other 8.033 r_scangle_other 6.862 r_mcangle_it 5.68 r_mcangle_other 5.679 r_scbond_it 5.142
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.062 r_dihedral_angle_4_deg 16.938 r_dihedral_angle_3_deg 16.081 r_dihedral_angle_1_deg 8.269 r_long_range_B_refined 8.034 r_long_range_B_other 8.033 r_scangle_other 6.862 r_mcangle_it 5.68 r_mcangle_other 5.679 r_scbond_it 5.142 r_scbond_other 5.141 r_mcbond_it 4.381 r_mcbond_other 4.381 r_angle_refined_deg 1.59 r_angle_other_deg 1.234 r_chiral_restr 0.065 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_gen_planes_other 0.003 r_bond_other_d 0.002 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 6395 Nucleic Acid Atoms Solvent Atoms 156 Heterogen Atoms 34
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling PHASER phasing