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Human transthyretin (TTR) complexed with 3-(9H-fluoren-9-ylideneaminooxy)propanoic acid in a dual binding mode
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3GS0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.7 293 protein: TTR 10 mg/ml + ligand 0.66 milli-M in 0.1 M NaCl, 0.05 M Na acetate, pH 5.5.
Precipitant: 70% (30% PEG-4K, 0.2 M imidazole malate, pH 6.0) and 30% (12% MPEG-5K, 0.1 M sodium acetate, pH 5.5).
Cryoprotectant: 40% (25 % diethylene glycol, 12.5 % MPD, 37.5 % 2,3-butanediol, 12.5 % 1,4-dioxane), 10% PEG 10K, 0.1 M (mixed sodium propionate, sodium cacodylate, Bis-Tris-propane) (65% component A pH 4; 35% B pH 9.5)
Crystal Properties Matthews coefficient Solvent content 2.15 42.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.25 α = 90 b = 86.37 β = 90 c = 63.34 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 ADSC QUANTUM 315r convex prefocussing mirror and a Kirkpatrick-Baez pair of focussing mirrors 2013-11-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 2 0.9801 SOLEIL PROXIMA 2
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 1.25 43.2 95.7 0.151 0.14 11.11 8.04 63728 -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 1.25 1.32 91.5 1.64 7.2
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 MOLECULAR REPLACEMENT THROUGHOUT 3GS0 1.25 35.72 1.34 63673 3181 95.6 0.174 0.173 0.1717 0.208 0.2068 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 14.139 f_angle_d 1.06 f_chiral_restr 0.044 f_bond_d 0.006 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1792 Nucleic Acid Atoms Solvent Atoms 265 Heterogen Atoms 54
Software Software Software Name Purpose PHENIX refinement MxCuBE data collection XDS data scaling Coot model building