3TCT

Structure of wild-type TTR in complex with tafamidis


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15.5THE 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 298.0K
Crystal Properties
Matthews coefficientSolvent content
2.1242

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.749α = 90
b = 84.994β = 90
c = 64.334γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-rayCCDMARMOSAIC 325 mm CCDFLAT MIRROR (VERTICAL FOCUSING)2010-02-19MSINGLE WAVELENGTH
21x-raySINGLE CRYSTAL SI(111) BENT MONOCHROMATOR (HO RIZONTAL FOCUSING)M
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL11-10.9795SSRLBL11-1

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
1,21.35099.40.03551.575830816.9
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)
1,21.31.3596.50.632.45.8

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 REPLACEMENTTHROUGHOUTpdb entry 2FBR1.35058122294099.40.1630.1610.192RANDOM20.4
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]
0.1-0.280.18
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.514
r_dihedral_angle_4_deg17.973
r_dihedral_angle_3_deg15.022
r_sphericity_free9.843
r_scangle_it6.206
r_dihedral_angle_1_deg5.993
r_sphericity_bonded5.349
r_scbond_it4.189
r_mcangle_it3.198
r_mcbond_it2.078
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.514
r_dihedral_angle_4_deg17.973
r_dihedral_angle_3_deg15.022
r_sphericity_free9.843
r_scangle_it6.206
r_dihedral_angle_1_deg5.993
r_sphericity_bonded5.349
r_scbond_it4.189
r_mcangle_it3.198
r_mcbond_it2.078
r_rigid_bond_restr2.056
r_angle_refined_deg1.682
r_angle_other_deg1.559
r_mcbond_other1.024
r_chiral_restr0.109
r_bond_refined_d0.019
r_gen_planes_refined0.01
r_bond_other_d0.003
r_gen_planes_other0.003
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1773
Nucleic Acid Atoms
Solvent Atoms141
Heterogen Atoms40

Software

Software
Software NamePurpose
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling