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Human thyroid hormone receptor alpha ligand binding domain in complex with beta-selective agonist ALG-055009
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3HZF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.1 M ADA pH 6.5, 1 M Ammoniumsulfate
Crystal Properties Matthews coefficient Solvent content 3.66 66.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 110.199 α = 90 b = 110.199 β = 90 c = 134.579 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 PIXEL DECTRIS EIGER X 16M 2019-12-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 0.9999 SLS X06SA
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) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.74 95.45 97.2 0.044 0.051 1 19.7 4.2 12868
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) Redundancy Number Unique Reflections (All) 1 2.74 2.99 98.5 0.45 0.515 0.859 3.33 4.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (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 Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.74 95.45 12118 750 97.17 0.19534 0.19348 0.199 0.22784 0.232 RANDOM
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] 0.44 0.22 0.44 -1.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.272 r_dihedral_angle_4_deg 16.144 r_dihedral_angle_3_deg 14.333 r_long_range_B_refined 12.45 r_long_range_B_other 12.447 r_scangle_other 10.292 r_mcangle_other 8.981 r_mcangle_it 8.976 r_scbond_it 7.384 r_scbond_other 7.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.272 r_dihedral_angle_4_deg 16.144 r_dihedral_angle_3_deg 14.333 r_long_range_B_refined 12.45 r_long_range_B_other 12.447 r_scangle_other 10.292 r_mcangle_other 8.981 r_mcangle_it 8.976 r_scbond_it 7.384 r_scbond_other 7.21 r_mcbond_it 6.052 r_mcbond_other 6.033 r_dihedral_angle_1_deg 5.976 r_angle_refined_deg 1.54 r_angle_other_deg 1.25 r_chiral_restr 0.083 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_bond_other_d 0.003 r_gen_planes_other 0.002 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 Atoms Number Protein Atoms 2052 Nucleic Acid Atoms Solvent Atoms 14 Heterogen Atoms 33
Software Software Software Name Purpose XDS data reduction XSCALE data scaling REFMAC refinement PHASER phasing