4TQI

Human transthyretin (TTR) complexed with 3-(9H-fluoren-9-ylideneaminooxy)propanoic acid in a dual binding mode


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3GS0 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.7293protein: 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 coefficientSolvent content
2.1542.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 43.25α = 90
b = 86.37β = 90
c = 63.34γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315rconvex prefocussing mirror and a Kirkpatrick-Baez pair of focussing mirrors2013-11-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSOLEIL BEAMLINE PROXIMA 20.9801SOLEILPROXIMA 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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.2543.295.70.1510.1411.118.0463728-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.251.3291.51.647.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3GS01.2535.721.3463673318195.60.1740.1730.208Random
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
KeyRefinement Restraint Deviation
f_dihedral_angle_d14.139
f_angle_d1.06
f_chiral_restr0.044
f_bond_d0.006
f_plane_restr0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1792
Nucleic Acid Atoms
Solvent Atoms265
Heterogen Atoms54

Software

Software
Software NamePurpose
PHENIXrefinement
MxCuBEdata collection
XDSdata scaling
Cootmodel building