3HZF

Structure of TR-alfa bound to selective thyromimetic GC-1 in C2 space group


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1BSX 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.22911.2M sodium acetate, 100mM sodium cacodylate, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.4549.73

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 89.799α = 90
b = 78.777β = 95.17
c = 43.071γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm plateOSMIC confocal Max-Flux2003-11-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU ULTRAX 181.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
12.544.7291.610.0760.0767.87.29551909222
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.52.6483.70.3660.3662.17.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1BSX2.544.729551909245991.610.191880.18840.26293RANDOM34.105
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]
3.79-2.55-2.55-1.7
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.844
r_scangle_it3.864
r_scbond_it2.438
r_angle_refined_deg1.813
r_mcangle_it1.448
r_mcbond_it0.739
r_nbd_refined0.241
r_symmetry_vdw_refined0.22
r_symmetry_hbond_refined0.215
r_xyhbond_nbd_refined0.14
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.844
r_scangle_it3.864
r_scbond_it2.438
r_angle_refined_deg1.813
r_mcangle_it1.448
r_mcbond_it0.739
r_nbd_refined0.241
r_symmetry_vdw_refined0.22
r_symmetry_hbond_refined0.215
r_xyhbond_nbd_refined0.14
r_chiral_restr0.107
r_bond_refined_d0.018
r_gen_planes_refined0.006
r_bond_other_d
r_angle_other_deg
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_gen_planes_other
r_nbd_other
r_nbtor_refined
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 Atoms2107
Nucleic Acid Atoms
Solvent Atoms19
Heterogen Atoms24

Software

Software
Software NamePurpose
MAR345dtbdata collection
AMoREphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling