3OZK

Crystal structure of human transthyretin variant A25T in complex with thyroxine (T4)


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52930.1M Hepes sodium pH 7.5, 28% PEG 400, 0.2 calcium chloride dihydrate, VAPOR DIFFUSION, HANGING DROP, temperature 293K, complex obtained by soaking crystal with ligand.
Crystal Properties
Matthews coefficientSolvent content
2.1442.61

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 43.13α = 90
b = 85.31β = 90
c = 64.34γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm plate2008-03-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONLNLS BEAMLINE W01B-MX21.4586LNLSW01B-MX2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
11.964.3499.80.0610.06117.64.1193501935023.3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.921000.260.262.84.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONTHROUGHOUT1.926.0118174114699.80.1910.1880.236RANDOM26.16
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]
2.51-1.42-1.1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.842
r_dihedral_angle_4_deg17.135
r_dihedral_angle_3_deg16.489
r_dihedral_angle_1_deg6.834
r_scangle_it4.818
r_scbond_it2.988
r_mcangle_it2.035
r_angle_refined_deg1.823
r_mcbond_it1.125
r_chiral_restr0.127
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.842
r_dihedral_angle_4_deg17.135
r_dihedral_angle_3_deg16.489
r_dihedral_angle_1_deg6.834
r_scangle_it4.818
r_scbond_it2.988
r_mcangle_it2.035
r_angle_refined_deg1.823
r_mcbond_it1.125
r_chiral_restr0.127
r_bond_refined_d0.018
r_gen_planes_refined0.009
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
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 Atoms1789
Nucleic Acid Atoms
Solvent Atoms142
Heterogen Atoms48

Software

Software
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
MAR345dtbdata collection
REFMACphasing