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Structure of E8 TCR in complex with human MR1 bound to 6FP
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 iodide, 0.1 M Bis-Tris propane pH 8.5 and 20 % w/v PEG 3350
Crystal Properties Matthews coefficient Solvent content 3.12 60.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.71 α = 90 b = 104.39 β = 90 c = 117.97 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 2.02 58.99 100 0.14 0.145 0.037 0.999 13.1 15.2 74899
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 2.02 2.05 100 4.786 4.946 1.234 0.299 0.6 15.7
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 2.02 58.99 71062 3762 99.97 0.236 0.23431 0.2436 0.26764 0.2771 RANDOM 53.513
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] -0.81 -1.78 2.59
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.038 r_dihedral_angle_3_deg 16.084 r_dihedral_angle_4_deg 15.476 r_dihedral_angle_1_deg 7.67 r_long_range_B_refined 5.447 r_long_range_B_other 5.435 r_mcangle_it 1.622 r_mcangle_other 1.621 r_angle_refined_deg 1.476 r_scangle_other 1.418
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.038 r_dihedral_angle_3_deg 16.084 r_dihedral_angle_4_deg 15.476 r_dihedral_angle_1_deg 7.67 r_long_range_B_refined 5.447 r_long_range_B_other 5.435 r_mcangle_it 1.622 r_mcangle_other 1.621 r_angle_refined_deg 1.476 r_scangle_other 1.418 r_angle_other_deg 1.215 r_mcbond_other 0.956 r_mcbond_it 0.955 r_scbond_other 0.893 r_scbond_it 0.892 r_chiral_restr 0.062 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 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 6369 Nucleic Acid Atoms Solvent Atoms 234 Heterogen Atoms 13
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling PHASER phasing