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Human transthyretin (TTR) complexed with (2,7-Dibromo-fluoren-9-ylideneaminooxy)-acetic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4PM1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 293 Protein: 10mg/ml in .1 M NaCl, .050 M Na acetate, pH 5.5.
Complex: 3 micro-L TTR + 3 micro-L 0.02% azide + 1 micro-L inhibitor (.001 M)
Precipitant: 18% PEG4K, 9% PEG10K, 0.12 M imidazole malate pH 6.0, 0.04 M ammonium acetate, pH 4.5.
Cryoprotectant: 10 % diethylene glycol + 5 % MPD + 15 % 2,3-butanediol + 5 % 1,4-dioxane, 12.5% MPEG 5K, 0.1 M mixed ( Na acetate, ADA, Bicine) 60% pH 4 / 40% pH 9)
Crystal Properties Matthews coefficient Solvent content 2.14 42.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.222 α = 90 b = 85.961 β = 90 c = 63.348 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 mirrors 2014-01-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.870060 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 1.41 50.996 99.9 0.088 0.083 17.26 9.09 46347 46322 -3
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 1.41 1.46 100 1.272 1.75 8.9
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 FREE R-VALUE 4PM1 1.41 42.981 1.34 46271 2343 99.94 0.1727 0.1714 0.1748 0.1973 0.1992 Random selection
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 14.41 f_angle_d 1.296 f_chiral_restr 0.082 f_plane_restr 0.011 f_bond_d 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1786 Nucleic Acid Atoms Solvent Atoms 196 Heterogen Atoms 25
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling REFMAC phasing Coot model building