5E4A

Human transthyretin (TTR) complexed with (2,7-Dichloro-fluoren-9-ylideneaminooxy)-acetic acid.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4TQ8 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.5293Protein: TTR at 5 mg/ml + 1.6 milli-M inhibitor. Precipitant: 18% PEG4K, 0.08M imidazole malate, pH 6.0 and 13.5% PEG10K, 0.06M ammonium acetate, pH 4.5 Cryoprotectant: 10% diethylene glycol + 5% MPD + 15% 2,3-butanediol + 5% 1,4-dioxane, 25% MPEG 5K, 0.1 M mixed (Na acetate, ADA, Bicine - 60% at pH 4/40% at pH 10) 1 milli-M inhibitor.
Crystal Properties
Matthews coefficientSolvent content
2.0138.84

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 43.21α = 90
b = 85.99β = 90
c = 63.82γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-Fmirrors2014-01-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-10.87006ESRFID23-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
11.3343.2199.90.0760.07214.929.125543055377-3
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)
11.331.3699.91.861.229.23

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 REPLACEMENTTHROUGHOUT4TQ81.3342.9952608276999.90.142020.139440.19239RANDOM24.215
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]
-0.690.310.38
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free45.611
r_dihedral_angle_2_deg30.932
r_sphericity_bonded18.658
r_dihedral_angle_4_deg15.784
r_dihedral_angle_3_deg15.012
r_rigid_bond_restr7.789
r_dihedral_angle_1_deg6.624
r_long_range_B_refined6.244
r_scbond_it4.285
r_mcangle_it3.625
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free45.611
r_dihedral_angle_2_deg30.932
r_sphericity_bonded18.658
r_dihedral_angle_4_deg15.784
r_dihedral_angle_3_deg15.012
r_rigid_bond_restr7.789
r_dihedral_angle_1_deg6.624
r_long_range_B_refined6.244
r_scbond_it4.285
r_mcangle_it3.625
r_mcbond_it2.867
r_angle_refined_deg2.452
r_chiral_restr0.188
r_bond_refined_d0.028
r_gen_planes_refined0.015
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1793
Nucleic Acid Atoms
Solvent Atoms267
Heterogen Atoms21

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
Cootmodel building