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Crystal Structure of Human Transthyretin in Complex with Perfluoroktansulfonsyra (PFOS)
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 sodiumphosphate buffer with 100 mM KCl pH 7.6 and concentrated to 5 mg per ml. PFOS 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 2.14 42.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.146 α = 90 b = 85.413 β = 90 c = 64.121 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 PIXEL DECTRIS PILATUS3 6M 2015-02-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.913 ESRF ID29
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 1.26 40 99.76 0.036 23.41 7.1 64626
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 1.26 1.3 98.83 0.565 2.97 6.5
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 1.26 38.511 1.34 64621 3183 99.75 0.1357 0.1345 0.1408 0.1583 0.1629
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 14.863 f_angle_d 1.332 f_chiral_restr 0.074 f_bond_d 0.009 f_plane_restr 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1792 Nucleic Acid Atoms Solvent Atoms 209 Heterogen Atoms 59
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing