4L1S

Covalent modification of transthyretin K15 by yielding the fluorescent conjugate (E)-3-(dimethylamino)-5-(4-hydroxy-3,5-dimethylstyryl)benzamide


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2FBR 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.5298The wt-TTR was concentrated to 4 mg/ml in 10 mM NaPi, 100 mM KCl, at pH 7.6 and co-crystallized at room temperature with inhibitors using the vapor-diffusion sitting drop method, crystals were grown from 1.395 M sodium citrate, 3.5% v/v glycerol at ph 5.5. The crystals were frozen using a cryo-protectant solution of 1.395 m sodium citrate, ph 5.5, containing 10% v/v glycerol, vapor diffusion, sitting drop, temperature 298.0, VAPOR DIFFUSION, SITTING DROP
Crystal Properties
Matthews coefficientSolvent content
2.0439.75

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 41.632α = 90
b = 86.059β = 90
c = 62.802γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray200PIXELPSI PILATUS 6MSINGLE CRYSTAL SI(111) BENT MONOCHROMATOR (HORIZONTAL FOCUSING)2012-08-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL12-20.9797SSRLBL12-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.537.4898.50.05918.66.13610312.6
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.51.5895.70.5375.95.95007

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 REPLACEMENTTHROUGHOUT2FBR1.537.4836009179697.950.16150.16020.1852RANDOM24.9124
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]
0.51-0.4-0.11
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.794
r_sphericity_free29.216
r_dihedral_angle_4_deg19.742
r_rigid_bond_restr17.386
r_dihedral_angle_3_deg15.944
r_sphericity_bonded12.428
r_dihedral_angle_1_deg6.215
r_mcangle_it3.607
r_angle_other_deg3.6
r_mcbond_it2.963
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.794
r_sphericity_free29.216
r_dihedral_angle_4_deg19.742
r_rigid_bond_restr17.386
r_dihedral_angle_3_deg15.944
r_sphericity_bonded12.428
r_dihedral_angle_1_deg6.215
r_mcangle_it3.607
r_angle_other_deg3.6
r_mcbond_it2.963
r_mcbond_other2.905
r_angle_refined_deg1.592
r_chiral_restr0.103
r_gen_planes_other0.096
r_gen_planes_refined0.048
r_bond_refined_d0.014
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1785
Nucleic Acid Atoms
Solvent Atoms138
Heterogen Atoms44

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
Blu-Icedata collection
XDSdata reduction
XDSdata scaling
PHASERphasing