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Structure of E8 TCR in complex in human MR1 K43A
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 0.2 M Magnesium chloride hexahydrate, 0.1 M Tris pH 8.5, 15 % PEG 4000
Crystal Properties Matthews coefficient Solvent content 3.13 60.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.24 α = 90 b = 111.38 β = 90 c = 143.5 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 2019-10-12 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 2.4 47.83 99.97 0.118 0.122 0.031 0.999 15.9 14.7 44778
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 2.4 2.44 96.55 1.487 1.561 0.463 0.499 1.4 10.8
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 2.4 44.03 42501 2211 99.8 0.19303 0.19074 0.2049 0.236 0.2401 RANDOM 57.395
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] 0.37 -0.29 -0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.141 r_dihedral_angle_3_deg 15.957 r_dihedral_angle_4_deg 13.075 r_dihedral_angle_1_deg 7.967 r_long_range_B_refined 6.816 r_long_range_B_other 6.815 r_scangle_other 4.985 r_mcangle_it 3.956 r_mcangle_other 3.955 r_scbond_it 3.256
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.141 r_dihedral_angle_3_deg 15.957 r_dihedral_angle_4_deg 13.075 r_dihedral_angle_1_deg 7.967 r_long_range_B_refined 6.816 r_long_range_B_other 6.815 r_scangle_other 4.985 r_mcangle_it 3.956 r_mcangle_other 3.955 r_scbond_it 3.256 r_scbond_other 3.255 r_mcbond_it 2.635 r_mcbond_other 2.634 r_angle_refined_deg 1.532 r_angle_other_deg 1.234 r_chiral_restr 0.065 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 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 6296 Nucleic Acid Atoms Solvent Atoms 231 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling PHASER phasing