2XN3

Crystal structure of thyroxine-binding globulin complexed with mefenamic acid


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2RIVPDB ENTRY 2RIV

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15.420% PEG3350, PH 5.4
Crystal Properties
Matthews coefficientSolvent content
2.3548

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 172.835α = 90
b = 41.624β = 90
c = 56.188γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray1002007-10-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU200

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
12.0921.9798.20.0914.55.2246922
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)
12.092.2188.50.323.33.3

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 REPLACEMENTTHROUGHOUTPDB ENTRY 2RIV2.0986.3923353125499.490.212840.210380.25957RANDOM32.786
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]
-0.53.2-2.71
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.172
r_dihedral_angle_3_deg14.074
r_dihedral_angle_4_deg14.03
r_dihedral_angle_1_deg6.317
r_scangle_it2.698
r_scbond_it1.69
r_angle_refined_deg1.258
r_mcangle_it1.172
r_angle_other_deg0.904
r_mcbond_it0.629
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.172
r_dihedral_angle_3_deg14.074
r_dihedral_angle_4_deg14.03
r_dihedral_angle_1_deg6.317
r_scangle_it2.698
r_scbond_it1.69
r_angle_refined_deg1.258
r_mcangle_it1.172
r_angle_other_deg0.904
r_mcbond_it0.629
r_mcbond_other0.122
r_chiral_restr0.07
r_bond_refined_d0.011
r_gen_planes_refined0.006
r_gen_planes_other0.006
r_bond_other_d0.002
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_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 Atoms2928
Nucleic Acid Atoms
Solvent Atoms130
Heterogen Atoms18

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALEPACKdata scaling
PHASERphasing