3IPE

Human Transthyretin (TTR) complexed with a palindromic bivalent amyloid inhibitor (7 carbon linker).


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2ROXPDB ENTRY 2ROX

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
14.529825- 32% v/v PEG550-monomethyl ether, 70 mM NaAc buffer pH 4-5 and 100 mM NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.1141.73

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 43.241α = 90
b = 84.876β = 90
c = 63.39γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC2006-09-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-2ESRFID14-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
11.44398.10.06216.57.445900216.8
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.41.4890.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)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 2ROX1.435.2643546231798.10.1760.1750.196RANDOM16.27
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]
0.09-0.01-0.08
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.118
r_dihedral_angle_4_deg19.311
r_dihedral_angle_3_deg13.693
r_dihedral_angle_1_deg5.862
r_scangle_it5.109
r_scbond_it3.231
r_mcangle_it2.393
r_angle_refined_deg1.382
r_mcbond_it1.342
r_rigid_bond_restr1.313
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.118
r_dihedral_angle_4_deg19.311
r_dihedral_angle_3_deg13.693
r_dihedral_angle_1_deg5.862
r_scangle_it5.109
r_scbond_it3.231
r_mcangle_it2.393
r_angle_refined_deg1.382
r_mcbond_it1.342
r_rigid_bond_restr1.313
r_angle_other_deg0.791
r_mcbond_other0.331
r_chiral_restr0.079
r_bond_refined_d0.01
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1778
Nucleic Acid Atoms
Solvent Atoms138
Heterogen Atoms45

Software

Software
Software NamePurpose
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling