3IPB

Human Transthyretin (TTR) complexed with a palindromic bivalent amyloid inhibitor (11 carbon linker).


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.529325- 32% v/v PEG550-monomethyl ether, 70 mM NaAc buffer pH 4-5 and 100 mM NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.0740.63

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.958α = 90
b = 84.681β = 90
c = 62.769γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42004-07-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-20.933ESRFID14-2

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
11.93893.50.07319.46.8209082.7
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)
1.92.0193.50.356.25.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT1.9381755295498.780.202450.200940.22909RANDOM14.643
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]
0.080.03-0.11
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.531
r_dihedral_angle_4_deg20.859
r_dihedral_angle_3_deg15.824
r_dihedral_angle_1_deg6.355
r_scangle_it6.207
r_scbond_it3.896
r_mcangle_it2.619
r_angle_refined_deg2.232
r_mcbond_it1.482
r_angle_other_deg1.025
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.531
r_dihedral_angle_4_deg20.859
r_dihedral_angle_3_deg15.824
r_dihedral_angle_1_deg6.355
r_scangle_it6.207
r_scbond_it3.896
r_mcangle_it2.619
r_angle_refined_deg2.232
r_mcbond_it1.482
r_angle_other_deg1.025
r_mcbond_other0.487
r_chiral_restr0.131
r_bond_refined_d0.028
r_gen_planes_refined0.012
r_bond_other_d0.002
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1778
Nucleic Acid Atoms
Solvent Atoms61
Heterogen Atoms98

Software

Software
Software NamePurpose
ADSCdata collection
MOLREPphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling