2QGE

Human transthyretin (TTR) complexed with 2-(3,5-Dimethylphenyl)benzoxazole


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2FBRHuman Transthyretin PDB 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 298.0K
Crystal Properties
Matthews coefficientSolvent content
2.3642.93

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.917α = 90
b = 85.777β = 90
c = 64.563γ = 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)2007-01-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL11-10.9791SSRLBL11-1

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
11.455099.90.0411.86.94296416.6
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)
11.451.51000.5673.46.84242

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 REPLACEMENTTHROUGHOUTHuman Transthyretin PDB 2FBR1.455042922216399.890.1660.1640.2RANDOM14.259
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]
0.12-0.05-0.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.416
r_dihedral_angle_4_deg19.288
r_dihedral_angle_3_deg13.886
r_sphericity_free10.713
r_dihedral_angle_1_deg6.118
r_scangle_it5.475
r_sphericity_bonded4.637
r_scbond_it4.122
r_mcangle_it3.04
r_mcbond_it2.484
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.416
r_dihedral_angle_4_deg19.288
r_dihedral_angle_3_deg13.886
r_sphericity_free10.713
r_dihedral_angle_1_deg6.118
r_scangle_it5.475
r_sphericity_bonded4.637
r_scbond_it4.122
r_mcangle_it3.04
r_mcbond_it2.484
r_rigid_bond_restr2.103
r_angle_refined_deg1.781
r_angle_other_deg1.028
r_mcbond_other0.947
r_nbd_refined0.222
r_nbd_other0.212
r_symmetry_vdw_other0.201
r_nbtor_refined0.183
r_symmetry_hbond_refined0.154
r_xyhbond_nbd_refined0.149
r_symmetry_vdw_refined0.146
r_chiral_restr0.113
r_nbtor_other0.09
r_bond_refined_d0.019
r_gen_planes_refined0.008
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1773
Nucleic Acid Atoms
Solvent Atoms148
Heterogen Atoms34

Software

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