2QGD

Human transthyretin (TTR) complexed with 2-(3,5-Dibromo-4-hydroxyphenyl)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
2.3642.91

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.945α = 90
b = 85.001β = 90
c = 65.097γ = 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 BL11-10.912SSRLBL11-1

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
11.55099.90.0621114.53843817.3
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)
11.51.531000.674.514.52511

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 2FBR1.55038380192499.320.1620.160.199RANDOM15.181
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]
0.28-0.21-0.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.067
r_dihedral_angle_4_deg17.412
r_dihedral_angle_3_deg13.986
r_sphericity_free9.974
r_dihedral_angle_1_deg6.037
r_scangle_it5.385
r_sphericity_bonded4.782
r_scbond_it4.419
r_mcangle_it3.02
r_mcbond_it2.521
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.067
r_dihedral_angle_4_deg17.412
r_dihedral_angle_3_deg13.986
r_sphericity_free9.974
r_dihedral_angle_1_deg6.037
r_scangle_it5.385
r_sphericity_bonded4.782
r_scbond_it4.419
r_mcangle_it3.02
r_mcbond_it2.521
r_rigid_bond_restr2.282
r_angle_refined_deg1.757
r_angle_other_deg0.932
r_mcbond_other0.925
r_nbd_other0.203
r_nbd_refined0.199
r_nbtor_refined0.18
r_symmetry_vdw_other0.172
r_symmetry_vdw_refined0.154
r_symmetry_hbond_refined0.151
r_xyhbond_nbd_refined0.145
r_chiral_restr0.111
r_nbtor_other0.088
r_bond_refined_d0.019
r_gen_planes_refined0.008
r_bond_other_d0.003
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1773
Nucleic Acid Atoms
Solvent Atoms142
Heterogen Atoms36

Software

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