8RQO | pdb_00008rqo

Human thyroid hormone receptor alpha ligand binding domain in complex with beta-selective agonist ALG-055009


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3HZF 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2930.1 M ADA pH 6.5, 1 M Ammoniumsulfate
Crystal Properties
Matthews coefficientSolvent content
3.6666.37

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 110.199α = 90
b = 110.199β = 90
c = 134.579γ = 120
Symmetry
Space GroupP 65 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2019-12-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06SA0.9999SLSX06SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim 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
12.7495.4597.20.0440.051119.74.212868
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.742.9998.50.450.5150.8593.334.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE2.7495.451211875097.170.195340.193480.1990.227840.232RANDOM
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]
0.440.220.44-1.43
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.272
r_dihedral_angle_4_deg16.144
r_dihedral_angle_3_deg14.333
r_long_range_B_refined12.45
r_long_range_B_other12.447
r_scangle_other10.292
r_mcangle_other8.981
r_mcangle_it8.976
r_scbond_it7.384
r_scbond_other7.21
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.272
r_dihedral_angle_4_deg16.144
r_dihedral_angle_3_deg14.333
r_long_range_B_refined12.45
r_long_range_B_other12.447
r_scangle_other10.292
r_mcangle_other8.981
r_mcangle_it8.976
r_scbond_it7.384
r_scbond_other7.21
r_mcbond_it6.052
r_mcbond_other6.033
r_dihedral_angle_1_deg5.976
r_angle_refined_deg1.54
r_angle_other_deg1.25
r_chiral_restr0.083
r_bond_refined_d0.012
r_gen_planes_refined0.006
r_bond_other_d0.003
r_gen_planes_other0.002
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2052
Nucleic Acid Atoms
Solvent Atoms14
Heterogen Atoms33

Software

Software
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
REFMACrefinement
PHASERphasing