3GS0

Human transthyretin (TTR) complexed with (S)-3-(9H-fluoren-9-ylideneaminooxy)-2-methylpropanoic acid (inhibitor 16)


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
2.244.16

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 43.39α = 90
b = 85.979β = 90
c = 65.076γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray120IMAGE PLATERIGAKU RAXIS IV++mirrors2007-02-02MSINGLE 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
11.8519.3798.692122421224
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.851.89897.45

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 1BMZ1.8519.372122420135108998.690.231650.231650.229640.2693RANDOM38.768
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]
1.58-1.46-0.11
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.967
r_dihedral_angle_3_deg19.289
r_dihedral_angle_4_deg18.864
r_dihedral_angle_1_deg6.487
r_scangle_it4.954
r_scbond_it3.316
r_mcangle_it2.276
r_angle_refined_deg2.227
r_mcbond_it1.504
r_nbtor_refined0.317
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.967
r_dihedral_angle_3_deg19.289
r_dihedral_angle_4_deg18.864
r_dihedral_angle_1_deg6.487
r_scangle_it4.954
r_scbond_it3.316
r_mcangle_it2.276
r_angle_refined_deg2.227
r_mcbond_it1.504
r_nbtor_refined0.317
r_symmetry_vdw_refined0.269
r_nbd_refined0.218
r_xyhbond_nbd_refined0.149
r_chiral_restr0.137
r_symmetry_hbond_refined0.136
r_bond_refined_d0.023
r_gen_planes_refined0.009
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1731
Nucleic Acid Atoms
Solvent Atoms138
Heterogen Atoms42

Software

Software
Software NamePurpose
CrystalCleardata collection
AMoREphasing
REFMACrefinement
CrystalCleardata reduction
CrystalCleardata scaling