3P3T

Human transthyretin (TTR) complexed with 4-(3-(2-flourophenoxy)propyl)-3,5-dimethyl-1H-pyrazole


X-RAY DIFFRACTION

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 298K
Crystal Properties
Matthews coefficientSolvent content
2.1342.31

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 43.009α = 90
b = 85.371β = 90
c = 64.006γ = 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), single crystal Si(111) bent monochromator (ho rizontal focusing)2010-02-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL11-10.97945SSRLBL11-1

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
11.455099.70.04239.97.24243425
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)
11.451.599.50.5873.16.64161

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 2FBR1.455042398214199.630.17040.16890.199RANDOM23.9801
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]
0.22-0.510.28
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.602
r_dihedral_angle_4_deg19.895
r_dihedral_angle_3_deg14.953
r_sphericity_free10.614
r_dihedral_angle_1_deg5.962
r_scangle_it5.932
r_sphericity_bonded5.411
r_scbond_it4.046
r_mcangle_it3.174
r_mcbond_it2.088
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.602
r_dihedral_angle_4_deg19.895
r_dihedral_angle_3_deg14.953
r_sphericity_free10.614
r_dihedral_angle_1_deg5.962
r_scangle_it5.932
r_sphericity_bonded5.411
r_scbond_it4.046
r_mcangle_it3.174
r_mcbond_it2.088
r_rigid_bond_restr2.088
r_angle_refined_deg1.772
r_angle_other_deg1.292
r_mcbond_other1.023
r_chiral_restr0.112
r_bond_refined_d0.019
r_gen_planes_refined0.01
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1779
Nucleic Acid Atoms
Solvent Atoms130
Heterogen Atoms36

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing