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Structure of E8 TCR in complex in human MR1 bound to 3FSA
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 Sodium malonate dibasic monohydrate, 0.1 M Bis-Tris Propane pH 8.5, 20% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.87 57.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.97 α = 90 b = 104.67 β = 90 c = 117.7 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 2020-07-09 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 2.09 58.85 99.77 0.091 0.094 0.024 1 14.9 15 67006
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 2.09 2.13 97.04 4.97 5.164 1.383 0.344 0.5 13.6
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 2.09 58.85 63556 3384 99.66 0.22714 0.22507 0.2316 0.26607 0.2696 RANDOM 69.852
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] -0.01 1.24 -1.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.287 r_dihedral_angle_4_deg 20.431 r_dihedral_angle_3_deg 16.175 r_dihedral_angle_1_deg 7.659 r_long_range_B_refined 4.828 r_long_range_B_other 4.821 r_scangle_other 2.916 r_mcangle_it 2.863 r_mcangle_other 2.863 r_scbond_it 1.849
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.287 r_dihedral_angle_4_deg 20.431 r_dihedral_angle_3_deg 16.175 r_dihedral_angle_1_deg 7.659 r_long_range_B_refined 4.828 r_long_range_B_other 4.821 r_scangle_other 2.916 r_mcangle_it 2.863 r_mcangle_other 2.863 r_scbond_it 1.849 r_scbond_other 1.846 r_mcbond_it 1.816 r_mcbond_other 1.815 r_angle_refined_deg 1.479 r_angle_other_deg 1.203 r_chiral_restr 0.06 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.003 r_gen_planes_other 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 6422 Nucleic Acid Atoms Solvent Atoms 77 Heterogen Atoms 11
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling PHASER phasing