2FBR

Human transthyretin (TTR) complexed with bivalant amyloid inhibitor (4 carbon linker)


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7289TTR bivalent inhibitor complexes of 1:1 stoichiometry resulting from coassembly at 5-7 mg/mL (95-133 microM in 100 mM KCl, 1 mM EDTA, 10 mM sodium phosphate, 0.35-0.50 M ammonium sulfate equilibrated against 2 M ammonium sulfate, pH 7.00, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
2.1442.43

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.599α = 90
b = 84.355β = 90
c = 65.569γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDSBC-32002-11-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-BM0.97918APS19-BM

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
11.4642.2697.73387943879438794
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.461.49894

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)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 1BMZ1.4642.2638794206297.730.210760.210760.210050.22356RANDOM17.399
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]
-0.770.110.65
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.225
r_scangle_it4.851
r_scbond_it3.01
r_mcangle_it2.167
r_angle_refined_deg1.721
r_angle_other_deg1.488
r_mcbond_it1.196
r_symmetry_vdw_other0.306
r_nbd_other0.267
r_nbd_refined0.198
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.225
r_scangle_it4.851
r_scbond_it3.01
r_mcangle_it2.167
r_angle_refined_deg1.721
r_angle_other_deg1.488
r_mcbond_it1.196
r_symmetry_vdw_other0.306
r_nbd_other0.267
r_nbd_refined0.198
r_xyhbond_nbd_refined0.161
r_symmetry_hbond_refined0.146
r_symmetry_vdw_refined0.129
r_chiral_restr0.126
r_nbtor_other0.087
r_bond_refined_d0.018
r_bond_other_d0.014
r_gen_planes_refined0.01
r_gen_planes_other0.01
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1770
Nucleic Acid Atoms
Solvent Atoms181
Heterogen Atoms37

Software

Software
Software NamePurpose
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement
HKL-2000data reduction
EPMRphasing