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Structure of E8 TCR in complex in human MR1 bound to 3FBA
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 Magnesium acetate tetrahydrate, 0.1 M MOPS pH 7.5, 12 % PEG 8000
Crystal Properties Matthews coefficient Solvent content 3.14 60.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.6 α = 90 b = 113.13 β = 90 c = 143.76 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 2019-11-30 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 2.29 50 100 0.233 0.241 0.062 0.998 9.5 15.1 51936
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 2.29 2.33 100 3.158 0.327 0.842 0.494 0.8 14.9
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5U6Q 2.29 50 49318 2550 99.98 0.21335 0.21079 0.26285 0.2428 RANDOM 54.187
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] 1.19 -2.51 1.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.756 r_dihedral_angle_3_deg 16.808 r_dihedral_angle_4_deg 13.19 r_long_range_B_refined 8.401 r_long_range_B_other 8.401 r_dihedral_angle_1_deg 8.298 r_scangle_other 6.803 r_mcangle_it 5.92 r_mcangle_other 5.919 r_scbond_it 4.972
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.756 r_dihedral_angle_3_deg 16.808 r_dihedral_angle_4_deg 13.19 r_long_range_B_refined 8.401 r_long_range_B_other 8.401 r_dihedral_angle_1_deg 8.298 r_scangle_other 6.803 r_mcangle_it 5.92 r_mcangle_other 5.919 r_scbond_it 4.972 r_scbond_other 4.972 r_mcbond_it 4.266 r_mcbond_other 4.266 r_angle_refined_deg 1.624 r_angle_other_deg 1.239 r_chiral_restr 0.068 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_gen_planes_other 0.003 r_bond_other_d 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 6344 Nucleic Acid Atoms Solvent Atoms 144 Heterogen Atoms 27
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling PHASER phasing