4L1T

Transthyretin in complex with (E)-3-(dimethylamino)-5-(4-hydroxy-3,5-dimethylstyryl)benzoic acid


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 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 298.0K
Crystal Properties
Matthews coefficientSolvent content
2.0740.55

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.305α = 90
b = 85.551β = 90
c = 63.006γ = 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
11.1637.9298.30.03420.367896014
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)
11.161.2290.50.6552.3510463

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 REPLACEMENTTHROUGHOUT2FBR1.1637.9278787393898.090.16480.16360.1879RANDOM18.4022
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]
0.62-0.11-0.5
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.502
r_dihedral_angle_4_deg18.565
r_dihedral_angle_3_deg13.191
r_sphericity_free9.313
r_sphericity_bonded6.3
r_dihedral_angle_1_deg6.066
r_scangle_it5.435
r_scbond_it3.63
r_mcangle_it3.091
r_mcbond_it1.948
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.502
r_dihedral_angle_4_deg18.565
r_dihedral_angle_3_deg13.191
r_sphericity_free9.313
r_sphericity_bonded6.3
r_dihedral_angle_1_deg6.066
r_scangle_it5.435
r_scbond_it3.63
r_mcangle_it3.091
r_mcbond_it1.948
r_rigid_bond_restr1.833
r_angle_refined_deg1.692
r_mcbond_other1.026
r_angle_other_deg0.951
r_chiral_restr0.105
r_bond_refined_d0.016
r_gen_planes_refined0.009
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1781
Nucleic Acid Atoms
Solvent Atoms179
Heterogen Atoms46

Software

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