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Crystal Structure of Human Thyroid Hormone Receptor beta LBD in complex with specific agonist GC-24
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Human Thyroid Hormone Receptor beta in complex with agonist GC-1; the crystal structure was solved in our lab, but not deposited at the PDB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.9 291 PEG 3350, sodium acetate, glucose, cymal-2, pH 4.9, VAPOR DIFFUSION, SITTING DROP, temperature 291.0K
Crystal Properties Matthews coefficient Solvent content 3.15 60.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.57 α = 90 b = 56.57 β = 90 c = 390.05 γ = 120
Symmetry Space Group P 65 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 4 2002-02-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 1.127 ALS 8.3.1
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) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.8 24.47 93 0.069 0.069 15.8 10076 9368 3 59.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.8 2.98 81.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT Human Thyroid Hormone Receptor beta in complex with agonist GC-1; the crystal structure was solved in our lab, but not deposited at the PDB 2.8 24.47 3 10075 9368 500 93 0.228 0.228 0.216 0.2244 0.264 0.2646 RANDOM 60.08
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] 8.9 14.57 8.9 -17.81
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 21.7 x_angle_deg 1.6 c_improper_angle_d 1.31 x_bond_d 0.011
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1892 Nucleic Acid Atoms Solvent Atoms 40 Heterogen Atoms 56
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling CNS refinement CNS phasing