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Crystal Structure of Human Transthyretin in Complex with 3,5,6-Trichloro-2-pyridinyloxyacetic acid (Triclopyr)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1F41
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.6 291 Purified TTRwt was dialyzed against 10 mM sodium phosphate buffer with 100 mM KCl pH 7.6 and concentrated to 5 mg per ml. Triclopyr was added at 5 x molar excess to the protein. The reservoir contained 1.3 to 1.6 M sodium citrate and 3.5 percent glycerol at pH 5.5. Drop size 3 plus 3 microliter
Crystal Properties Matthews coefficient Solvent content 2.11 41.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.543 α = 90 b = 85.52 β = 90 c = 64.012 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD Bruker Platinum 135 2016-05-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER AXS MICROSTAR-H 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.58 27.3 94.8 0.081 9.4 3.1 31035
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.58 1.68 87.4 0.691 1.4 2.8
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 1F41 1.581 27.282 1.33 31035 2792 90.99 0.1615 0.1596 0.1649 0.1982 0.2025
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 14.279 f_angle_d 0.654 f_chiral_restr 0.052 f_plane_restr 0.006 f_bond_d 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1785 Nucleic Acid Atoms Solvent Atoms 204 Heterogen Atoms 29
Software Software Software Name Purpose PHENIX refinement SAINT data reduction SADABS data scaling PHASER phasing