☰ Navigation Tabs
Human transthyretin (TTR) complexed with 3-(9H-fluoren-9-ylideneaminooxy)ethanoic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4TQ8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.7 293 protein: 5 mg/ml 0.05 M NaCl, 0.05 M Na acetate, pH 5.5 with 1 milli-M ligand.
Precipitant: 60% (30% PEG-4K, 0.2 M imidazole malate, pH 6.0) and 40% (24% MPEG-5K, 0.1M sodium acetate, pH 5.5).
Cryoprotectant: 40% (25 % diethylene glycol, 12.5 % MPD, 37.5 % 2,3-butanediol, 12.5 % 1,4-dioxane), 12.5% MPEG 5K, 25% MPEG 550, 100 mM (sodium propionate, sodium cacodylate, Bis-Tris-propane(50% component A pH 4; 50% B pH 9.5) and 1 mM ligand.
Crystal Properties Matthews coefficient Solvent content 2.09 41.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.44 α = 90 b = 85.96 β = 90 c = 63 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 PILATUS 6M-F 2014-01-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.87006 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.51 43 99.9 0.122 0.121 12.8 9.13 36880 36840 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.51 1.6 99.7 0.7 9.34
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT 4TQ8 1.511 38.055 1.33 36829 1841 99.88 0.1872 0.1853 0.1879 0.222 0.2245 Random
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 15.623 f_angle_d 1.639 f_chiral_restr 0.049 f_bond_d 0.007 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1810 Nucleic Acid Atoms Solvent Atoms 322 Heterogen Atoms 42
Software Software Software Name Purpose PHENIX refinement Coot model building XDS data scaling MxCuBE data collection