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Crystal structure of TCR-017 ectodomain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5C0B
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 0.1M Hepes (pH 7.0), 1.1M sodium malonate
Crystal Properties Matthews coefficient Solvent content 2.61 52.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.049 α = 90 b = 81.175 β = 90 c = 315.105 γ = 90
Symmetry Space Group C 2 2 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 95 PIXEL DECTRIS EIGER X 4M 2021-02-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-1A 1.07 Photon Factory BL-1A
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 2.18 46.37 99.8 0.093 0.1 0.038 0.998 13.7 6.8 371960 40.7213355473
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 2.18 2.3 99.6 0.816 0.88 0.328 0.819 2.3 7.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5C0B 2.18000239315 42.4180059693 1.35593010334 54612 2757 99.7479452055 0.224406282572 0.221625461106 0.222 0.276115701106 0.2763 42.0962422147
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 8.64620548006 f_angle_d 1.03754615808 f_chiral_restr 0.0549053737874 f_bond_d 0.0083499826573 f_plane_restr 0.00616188637141
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6854 Nucleic Acid Atoms Solvent Atoms 307 Heterogen Atoms
Software Software Software Name Purpose PHENIX data reduction PHENIX refinement Coot model building SCALA data scaling MOLREP phasing