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Human thyroid hormone receptor beta 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 3JZC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 1.40 M NaAcetate, 0.10 M NaCacodylate pH 7.0
Crystal Properties Matthews coefficient Solvent content 2.77 55.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.563 α = 90 b = 68.563 β = 90 c = 129.725 γ = 120
Symmetry Space Group P 31 2 1
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 2020-02-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.9999 SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) Rpim 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 2.88 59.38 91.9 0.057 0.016 1 22.4 12 7714
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.88 3.01 0.871 0.451 0.8
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 2.88 59.38 7340 374 91.87 0.2179 0.21573 0.2163 0.26237 0.256 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] 1.14 0.57 1.14 -3.69
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.587 r_dihedral_angle_3_deg 13.01 r_dihedral_angle_4_deg 12.093 r_scangle_other 11.075 r_mcangle_it 9.867 r_mcangle_other 9.863 r_scbond_it 7.884 r_scbond_other 7.882 r_mcbond_it 6.841 r_mcbond_other 6.841
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.587 r_dihedral_angle_3_deg 13.01 r_dihedral_angle_4_deg 12.093 r_scangle_other 11.075 r_mcangle_it 9.867 r_mcangle_other 9.863 r_scbond_it 7.884 r_scbond_other 7.882 r_mcbond_it 6.841 r_mcbond_other 6.841 r_dihedral_angle_1_deg 6.156 r_angle_refined_deg 1.426 r_angle_other_deg 1.21 r_chiral_restr 0.072 r_bond_refined_d 0.011 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 1980 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 28
Software Software Software Name Purpose autoPROC data reduction XDS data reduction autoPROC data scaling Aimless data scaling REFMAC refinement XSCALE data scaling PHASER phasing