7QDT

Crystal structure of a mutant (P393GX) Thyroid Receptor Alpha ligand binding domain designed to model dominant negative human mutations.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2H79 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.52930.2 M Sodium Chloride, 0.1 M Tris pH 8.5, 1.0 M Lithium Sulphate
Crystal Properties
Matthews coefficientSolvent content
2.3547.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 143.328α = 90
b = 143.328β = 90
c = 88.502γ = 120
Symmetry
Space GroupP 64 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2015-10-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I240.9690DiamondI24

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)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
1372.061000.1350.1390.0340.9992216.511208
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
133.181000.70.7210.170.9485.3

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 REPLACEMENTTHROUGHOUT2h79372.061120858199.860.185550.183220.22754RANDOM52.545
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]
-2.26-1.13-2.267.34
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.475
r_dihedral_angle_4_deg21.251
r_dihedral_angle_3_deg17.853
r_long_range_B_other9.604
r_long_range_B_refined9.603
r_scangle_other7.948
r_dihedral_angle_1_deg7.194
r_mcangle_it6.394
r_mcangle_other6.393
r_scbond_it5.276
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.475
r_dihedral_angle_4_deg21.251
r_dihedral_angle_3_deg17.853
r_long_range_B_other9.604
r_long_range_B_refined9.603
r_scangle_other7.948
r_dihedral_angle_1_deg7.194
r_mcangle_it6.394
r_mcangle_other6.393
r_scbond_it5.276
r_scbond_other5.273
r_mcbond_it4.324
r_mcbond_other4.295
r_angle_refined_deg2.059
r_angle_other_deg0.977
r_chiral_restr0.103
r_bond_refined_d0.016
r_gen_planes_refined0.007
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 Atoms1854
Nucleic Acid Atoms
Solvent Atoms9
Heterogen Atoms23

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing