3KGU | pdb_00003kgu

Wild type human transthyretin (TTR) complexed with genistein (TTRwt:GEN) pH 7.5


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52930.2 M CaCl2, 0.1 M HEPES pH 7.5, 28% PEG 400, vapor diffusion, hanging drop, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.3347.16

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 43.53α = 90
b = 85.35β = 90
c = 64.97γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2009-03-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONLNLS BEAMLINE W01B-MX21.4586LNLSW01B-MX2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.853094.64.421450

Refinement

Statistics
Diffraction IDStructure Solution MethodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)Mean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENT1.8521.420208103594.60.1990.1970.20.2340.2321.36
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]
0.02-0.01-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.168
r_dihedral_angle_3_deg13.22
r_dihedral_angle_4_deg7.739
r_dihedral_angle_1_deg5.546
r_scangle_it2.447
r_scbond_it1.498
r_mcangle_it1.149
r_angle_refined_deg1.14
r_mcbond_it0.623
r_nbtor_refined0.306
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.168
r_dihedral_angle_3_deg13.22
r_dihedral_angle_4_deg7.739
r_dihedral_angle_1_deg5.546
r_scangle_it2.447
r_scbond_it1.498
r_mcangle_it1.149
r_angle_refined_deg1.14
r_mcbond_it0.623
r_nbtor_refined0.306
r_nbd_refined0.204
r_symmetry_vdw_refined0.175
r_symmetry_hbond_refined0.15
r_xyhbond_nbd_refined0.135
r_chiral_restr0.075
r_bond_refined_d0.009
r_gen_planes_refined0.005
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 Atoms1778
Nucleic Acid Atoms
Solvent Atoms146
Heterogen Atoms40

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction