3GS7

Human transthyretin (TTR) complexed with (E)-3-(2-methoxybenzylideneaminooxy)propanoic acid (inhibitor 13)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1BMZPDB entry 1BMZ

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7290Crystals of wt-TTR were obtained from 5-7 mg/mL protein solutions (in 100 mM KCl, 1 mM EDTA, 10 mM sodium phosphate, pH 7.0, 0.3 M ammonium sulfate) equilibrated against 2 M ammonium sulfate in hanging drops. All TTR:ligand complexes were prepared from crystals soaked with a ten fold molar excess of ligand for more than three weeks. , VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal Properties
Matthews coefficientSolvent content
2.0740.55

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.169α = 90
b = 84.757β = 90
c = 63.807γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray120IMAGE PLATERIGAKU RAXIS IV++Mirrors2008-01-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-0071.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.820.1198.962164821648
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.81.84793.97

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 1BMZ1.820.112166820553111598.960.226850.226850.224710.26581RANDOM40.261
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]
0.44-1.380.95
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.942
r_dihedral_angle_3_deg17.126
r_dihedral_angle_4_deg6.548
r_dihedral_angle_1_deg6.034
r_scangle_it5.127
r_scbond_it3.374
r_mcangle_it2.404
r_angle_refined_deg1.924
r_mcbond_it1.502
r_nbtor_refined0.319
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.942
r_dihedral_angle_3_deg17.126
r_dihedral_angle_4_deg6.548
r_dihedral_angle_1_deg6.034
r_scangle_it5.127
r_scbond_it3.374
r_mcangle_it2.404
r_angle_refined_deg1.924
r_mcbond_it1.502
r_nbtor_refined0.319
r_nbd_refined0.224
r_symmetry_vdw_refined0.211
r_symmetry_hbond_refined0.146
r_xyhbond_nbd_refined0.144
r_chiral_restr0.127
r_bond_refined_d0.019
r_gen_planes_refined0.008
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1731
Nucleic Acid Atoms
Solvent Atoms143
Heterogen Atoms32

Software

Software
Software NamePurpose
CrystalCleardata collection
AMoREphasing
REFMACrefinement
CrystalCleardata reduction
CrystalCleardata scaling