4X30

Crystal structure of human Thyroxine-binding globulin complexed with thyroine at 1.55 Angstrom resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2CEO 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1EVAPORATION7.4293PEG3350, (NH4)2SO4, NaCl, Tris-HCl
Crystal Properties
Matthews coefficientSolvent content
2.652.64

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 65.46α = 90
b = 65.46β = 90
c = 202.71γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M2013-06-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL17U0.97930SSRFBL17U

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
11.5534.5990.06812.74.564376
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.551.581000.731.94.3

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 REPLACEMENTTHROUGHOUT2ceo1.5534.4960985326098.730.184420.183330.2048RANDOM20.883
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]
0.530.53-1.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.68
r_dihedral_angle_4_deg16.578
r_dihedral_angle_3_deg12.854
r_dihedral_angle_1_deg5.89
r_long_range_B_refined5.271
r_long_range_B_other5.271
r_scangle_other2.114
r_mcangle_other1.637
r_mcangle_it1.636
r_scbond_it1.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.68
r_dihedral_angle_4_deg16.578
r_dihedral_angle_3_deg12.854
r_dihedral_angle_1_deg5.89
r_long_range_B_refined5.271
r_long_range_B_other5.271
r_scangle_other2.114
r_mcangle_other1.637
r_mcangle_it1.636
r_scbond_it1.31
r_scbond_other1.308
r_angle_refined_deg1.307
r_mcbond_it0.972
r_mcbond_other0.967
r_angle_other_deg0.713
r_chiral_restr0.076
r_bond_refined_d0.008
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2935
Nucleic Acid Atoms
Solvent Atoms365
Heterogen Atoms42

Software

Software
Software NamePurpose
REFMACrefinement
Cootmodel building
MOSFLMdata processing
PHASERphasing
SCALAdata reduction
SCALEPACKdata scaling