2TRH

TERTIARY STRUCTURES OF THREE AMYLOIDOGENIC TRANSTHYRETIN VARIANTS AND IMPLICATIONS FOR AMYLOID FIBRIL FORMATION


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1TTAPDB ENTRY 1TTA

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.5PURIFIED PROTEIN (20MG/ML IN 100MM TRIS BUFFER, PH 7.5) WAS CRYSTALLIZED FROM\\ 2.25M AMMONIUM SULFATE, 100MM CITRATE BUFFER, PH 5.5 AT ROOM TEMPERATURE.\\, pH 6.5
Crystal Properties
Matthews coefficientSolvent content
2.252.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 43.38α = 90
b = 86.34β = 90
c = 65.58γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray296IMAGE PLATERIGAKU RAXIS IICCOLLIMATOR1995-06-27M
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RUH2R

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
11.852.2288.60.1090.07354.320855111.6
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.81.8674.70.270.221.92

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 REPLACEMENTTHROUGHOUTPDB ENTRY 1TTA1.95216842100989.30.2190.2190.299RANDOM22.6
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
x_dihedral_angle_d25.9
x_angle_deg1.87
x_scangle_it1.58
x_improper_angle_d1.57
x_mcangle_it1.41
x_scbond_it1.41
x_mcbond_it1.22
x_bond_d0.011
x_bond_d_na
x_bond_d_prot
RMS Deviations
KeyRefinement Restraint Deviation
x_dihedral_angle_d25.9
x_angle_deg1.87
x_scangle_it1.58
x_improper_angle_d1.57
x_mcangle_it1.41
x_scbond_it1.41
x_mcbond_it1.22
x_bond_d0.011
x_bond_d_na
x_bond_d_prot
x_angle_d
x_angle_d_na
x_angle_d_prot
x_angle_deg_na
x_angle_deg_prot
x_dihedral_angle_d_na
x_dihedral_angle_d_prot
x_improper_angle_d_na
x_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1954
Nucleic Acid Atoms
Solvent Atoms71
Heterogen Atoms

Software

Software
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
bioteXdata reduction
bioteXdata scaling
X-PLORphasing