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Structure of E8 TCR in complex with human MR1 bound to 5-OP-RU
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4PJ7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.2 M Potassium thiocyanate, 0.1 M Bis-Tris Propane pH 8.5, 20 % PEG 3350
Crystal Properties Matthews coefficient Solvent content 3.13 60.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.19 α = 90 b = 103.85 β = 90 c = 117.86 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 2020-02-24 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 2.4 59.24 99.12 0.133 0.137 0.035 0.999 13.8 15.2 44054
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 98.17 3.872 4.022 1.073 0.419 0.8
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 4PJ7 2.4 59.24 41848 2160 99.01 0.21856 0.21548 0.2259 0.27621 0.2812 RANDOM 78.013
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] 0.78 3.36 -4.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.615 r_dihedral_angle_3_deg 18.42 r_dihedral_angle_4_deg 16.75 r_dihedral_angle_1_deg 7.823 r_long_range_B_refined 3.746 r_long_range_B_other 3.746 r_mcangle_it 2.288 r_mcangle_other 2.287 r_scangle_other 2.143 r_angle_refined_deg 1.559
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.615 r_dihedral_angle_3_deg 18.42 r_dihedral_angle_4_deg 16.75 r_dihedral_angle_1_deg 7.823 r_long_range_B_refined 3.746 r_long_range_B_other 3.746 r_mcangle_it 2.288 r_mcangle_other 2.287 r_scangle_other 2.143 r_angle_refined_deg 1.559 r_mcbond_it 1.386 r_mcbond_other 1.386 r_scbond_it 1.31 r_scbond_other 1.31 r_angle_other_deg 1.19 r_chiral_restr 0.065 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 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 6362 Nucleic Acid Atoms Solvent Atoms 55 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling PHASER phasing