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Structure of TCR in complex with peptide-HLA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5E00 experimental model PDB 4OZI experimental model PDB 4QRP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.2 M Sodium citrate tribasic dihydrate, 0.1 M Bis-Tris propane pH 7.5, and 20 % w/v PEG 3350
Crystal Properties Matthews coefficient Solvent content 3.56 65.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.12 α = 90 b = 93.53 β = 90 c = 388.95 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 2021-05-14 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 2.77 90.94 99.62 0.212 0.22 0.057 0.998 8.1 14.4 69770
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 2.77 2.82 94.03 3.438 3.642 1.158 0.366 0.3 9.2
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 2.77 90.94 66086 3484 99.33 0.21976 0.21709 0.237 0.27357 0.2861 RANDOM 108.509
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] 5.4 -0.02 -5.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 19.404 r_long_range_B_refined 11.065 r_long_range_B_other 11.065 r_dihedral_angle_2_deg 9.41 r_dihedral_angle_1_deg 8.37 r_scangle_other 8.243 r_mcangle_it 7.803 r_mcangle_other 7.802 r_scbond_it 5.186 r_scbond_other 5.186
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 19.404 r_long_range_B_refined 11.065 r_long_range_B_other 11.065 r_dihedral_angle_2_deg 9.41 r_dihedral_angle_1_deg 8.37 r_scangle_other 8.243 r_mcangle_it 7.803 r_mcangle_other 7.802 r_scbond_it 5.186 r_scbond_other 5.186 r_mcbond_it 4.991 r_mcbond_other 4.99 r_angle_refined_deg 1.767 r_angle_other_deg 0.607 r_chiral_restr 0.081 r_bond_refined_d 0.007 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 13154 Nucleic Acid Atoms Solvent Atoms 11 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling PHASER phasing