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Human transthyretin (TTR) complexed with curcumin
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 7.5 293 Precipitant: 40% MPEG 2,000, 1% dioxane, 0.1 M sodium cacodylate, pH 7.5.
Cryoprotectant: 40% mixed (25% dioxane, 25% DMSO, 12.5% ethylene glycol, 12.5% 1,2-propanediol, 12.5% glycerol, 12.5% 2,3-butanediol) 50% (25% MPEG 5K, 0.1 M mixed (sodium acetate, ADA, bicine 20% pH 4 and 80% pH 9), 3 milli-M Curcumin for 20 min
Crystal Properties Matthews coefficient Solvent content 2.31 46.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.255 α = 90 b = 85.487 β = 90 c = 64.168 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 bent cylindrical mirror 2014-04-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.9793 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 1.35 39 99.9 0.065 0.061 18.07 8.95 53047 52995 -3 16.55
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 1.35 1.4 99.9 1.94 9.03
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4PM1 1.35 39 1.35 52990 2690 99.9 0.1777 0.1761 0.2088 0.2082 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 14.767 f_angle_d 1.258 f_chiral_restr 0.047 f_bond_d 0.007 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1811 Nucleic Acid Atoms Solvent Atoms 220 Heterogen Atoms 59
Software Software Software Name Purpose PHENIX refinement XDS data scaling XSCALE data scaling REFMAC refinement Coot model building ADSC data collection