4HIS

The Structure of V122I Mutant Transthyretin in Complex with Tafamidis


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 298K
Crystal Properties
Matthews coefficientSolvent content
2.141.55

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.673α = 90
b = 84.601β = 90
c = 64.317γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-rayPIXELPSI PILATUS 6MRh coated flat mirror2012-06-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL11-10.9797SSRLBL11-1

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
11.264.3299.60.028266.27311013.8

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 REPLACEMENTTHROUGHOUT2FBR1.264.3273015367999.440.15410.15310.172RANDOM20.0954
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]
0.61-0.15-0.46
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.198
r_dihedral_angle_4_deg17.745
r_dihedral_angle_3_deg14.192
r_scangle_it6.409
r_dihedral_angle_1_deg6.238
r_scbond_it4.289
r_mcangle_it3.355
r_mcbond_it2.118
r_rigid_bond_restr1.857
r_angle_refined_deg1.746
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.198
r_dihedral_angle_4_deg17.745
r_dihedral_angle_3_deg14.192
r_scangle_it6.409
r_dihedral_angle_1_deg6.238
r_scbond_it4.289
r_mcangle_it3.355
r_mcbond_it2.118
r_rigid_bond_restr1.857
r_angle_refined_deg1.746
r_angle_other_deg0.959
r_mcbond_other0.677
r_chiral_restr0.109
r_bond_refined_d0.017
r_gen_planes_refined0.009
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1781
Nucleic Acid Atoms
Solvent Atoms229
Heterogen Atoms20

Software

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