2CEO

thyroxine-binding globulin complex with thyroxine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1YXAPDB ENTRY 1YXA

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.410MM TRIS-HCL, 50MM NACL, 1MM EDTA PH 7.4, 20% PEG 3350, 0.2M NAF, 5% GLYCEROL
Crystal Properties
Matthews coefficientSolvent content
2.2746

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 73.404α = 90
b = 88.022β = 90
c = 124.118γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCDMIRRORS2005-11-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSRS BEAMLINE PX14.2SRSPX14.2

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
12.830.1493.60.29.6513.819138-538.1
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)
12.82.9564.80.52.24

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 REPLACEMENTTHROUGHOUTPDB ENTRY 1YXA2.830.141816697293.60.2370.2350.283RANDOM8.19
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]
-3.345.53-2.19
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.114
r_dihedral_angle_3_deg16.015
r_dihedral_angle_4_deg10.059
r_dihedral_angle_1_deg5.78
r_mcangle_it2.372
r_scangle_it2.168
r_mcbond_it1.441
r_scbond_it1.429
r_angle_refined_deg1.011
r_nbtor_refined0.298
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.114
r_dihedral_angle_3_deg16.015
r_dihedral_angle_4_deg10.059
r_dihedral_angle_1_deg5.78
r_mcangle_it2.372
r_scangle_it2.168
r_mcbond_it1.441
r_scbond_it1.429
r_angle_refined_deg1.011
r_nbtor_refined0.298
r_symmetry_vdw_refined0.267
r_symmetry_hbond_refined0.259
r_nbd_refined0.184
r_xyhbond_nbd_refined0.129
r_chiral_restr0.068
r_bond_refined_d0.007
r_gen_planes_refined0.002
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_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5798
Nucleic Acid Atoms
Solvent Atoms26
Heterogen Atoms60

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing