2GAB

Human Transthyretin (TTR) Complexed with Hydroxylated polychlorinated Biphenyl-4-hydroxy-3,3',5,4'-tetrachlorobiphenyl


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1BMZ 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7298CRYSTALLIZATION CONDITIONS: CRYSTALS OF RECOMBINANT WT TTR WERE OBTAINED FROM PROTEIN SOLUTIONS AT 5 MG/ML (IN 100 MM KCL, 100 MM PHOSPHATE [PH 7.4], 1 M AMMONIUM SULFATE) EQUILIBRATED AGAINST 2 M AMMONIUM SULFATE IN HANGING DROP EXPERIMENTS. THE TTR LIGAND COMPLEXES WERE PREPARED FROM CRYSTALS SOAKED FOR 2 WEEKS WITH A 10-FOLD MOLAR EXCESS , PH 7.00, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K , VAPOR DIFFUSION, HANGING DROP
Crystal Properties
Matthews coefficientSolvent content
2.2244.71

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 43.459α = 90
b = 86.197β = 90
c = 65.488γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray120IMAGE PLATEMAC Science DIP-20301999-07-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
11.8565.5189.20.031913319133
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.81.8692.35

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1BMZ1.8565.51191331814598888.220.211470.211470.210080.23769RANDOM23.974
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]
0.120.03-0.15
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.822
r_dihedral_angle_4_deg26.403
r_dihedral_angle_3_deg14.456
r_dihedral_angle_1_deg5.676
r_scangle_it5.293
r_scbond_it3.26
r_angle_refined_deg2.272
r_mcangle_it2.105
r_mcbond_it1.101
r_nbtor_refined0.311
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.822
r_dihedral_angle_4_deg26.403
r_dihedral_angle_3_deg14.456
r_dihedral_angle_1_deg5.676
r_scangle_it5.293
r_scbond_it3.26
r_angle_refined_deg2.272
r_mcangle_it2.105
r_mcbond_it1.101
r_nbtor_refined0.311
r_nbd_refined0.194
r_symmetry_vdw_refined0.179
r_xyhbond_nbd_refined0.109
r_chiral_restr0.107
r_symmetry_hbond_refined0.102
r_gen_planes_refined0.065
r_bond_refined_d0.016
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1731
Nucleic Acid Atoms
Solvent Atoms75
Heterogen Atoms34

Software

Software
Software NamePurpose
HKL-2000data collection
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement
HKL-2000data reduction