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Crystal structure of S2c-a5b6 TCR in complex with CD1c
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3OV6 experimental model PDB 4P4K experimental model PDB 5FK9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.2 M Sodium thiocyanate and 20 % (w/v) PEG 3350
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.233 α = 91.85 b = 83.652 β = 95.99 c = 180.13 γ = 115.61
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 2024-04-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9537 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 2.27 89.24 98.52 0.101 0.119 0.063 0.963 14.6 3.6 194208
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 2.27 2.31 96.77 1.66 1.943 1.004 0.325 0.8 3.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.27 89.24 192181 2022 98.52 0.22653 0.22626 0.239 0.25287 0.2672 RANDOM 72.912
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] 3.15 1.25 -0.46 -1.64 1.85 -2.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.935 r_dihedral_angle_2_deg 11.622 r_long_range_B_refined 7.94 r_long_range_B_other 7.94 r_dihedral_angle_1_deg 7.599 r_scangle_other 5.646 r_mcangle_it 4.811 r_mcangle_other 4.81 r_scbond_it 3.659 r_scbond_other 3.659
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.935 r_dihedral_angle_2_deg 11.622 r_long_range_B_refined 7.94 r_long_range_B_other 7.94 r_dihedral_angle_1_deg 7.599 r_scangle_other 5.646 r_mcangle_it 4.811 r_mcangle_other 4.81 r_scbond_it 3.659 r_scbond_other 3.659 r_mcbond_it 3.088 r_mcbond_other 3.088 r_angle_refined_deg 1.63 r_angle_other_deg 0.585 r_chiral_restr 0.117 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_dihedral_angle_4_deg 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 25763 Nucleic Acid Atoms Solvent Atoms 82 Heterogen Atoms 332
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling PHASER phasing