4PM1

Human transthyretin (TTR) complexed with 16-alpha-bromo-estradiol


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3GS4 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.2293Protein: 5 mg/ml TTR dialysed against 0.1 M NaCl, 0.05M Na acetate, pH 5.5. Precipitant:: 70% (30% PEG 4000, 0.2M imidazole malate, pH 6.0) 30% (18% monomethyl PEG 2000, 0.1 M sodium cacodylate, pH 6.5). Cryoprotectant: 40% (25 % diethylene glycol + 12.5 % MPD + 37.5 % 2,3-butanediol + 12.5 % 1,4-dioxane) 50% (12.5% MPEG 5K, 25% MPEG 550) 0.1 M (mixed Na propionate, Na cacodylate, Bis-Tris-propane 50% at pH 4.0 and 50% pH 9.5)
Crystal Properties
Matthews coefficientSolvent content
2.1442.53

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 43.202α = 90
b = 86.134β = 90
c = 63.395γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2014-01-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-10.87ESRFID23-1

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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.2343.067980.1180.11111.739.326950568116-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.231.2796.41.221.889.58

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 REPLACEMENTTHROUGHOUT3GS41.2343.0671.34680633416980.17840.17670.2106Random
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_d16.062
f_angle_d1.304
f_chiral_restr0.05
f_bond_d0.007
f_plane_restr0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1794
Nucleic Acid Atoms
Solvent Atoms334
Heterogen Atoms50

Software

Software
Software NamePurpose
PHENIXrefinement
REFMACrefinement
Cootmodel building
XDSdata scaling
XSCALEdata scaling
ADSCdata collection