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An agonist(compound 14e)of Thyroid Hormone Receptor B
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6KKB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 1.3 M ammonium sulfate, 0.1 M MES monohydrate pH 6.7 and 13% v/v 1,4-Dioxane
Crystal Properties Matthews coefficient Solvent content 3.11 60.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.552 α = 90 b = 82.552 β = 90 c = 211.698 γ = 90
Symmetry Space Group P 43 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 PILATUS3 S 6M 2021-05-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 1.000 SSRF BL19U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.698 50 100 0.11 0.115 0.034 0.993 6.7 12.7 21049
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.7 2.75 100 1.332 1.385 0.375 0.829 13.5
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.698 45.019 19595 930 93.261 0.226 0.2235 0.2252 0.2748 0.2734 57.16
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] -0.444 -0.444 0.887
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.144 r_dihedral_angle_3_deg 22.033 r_dihedral_angle_4_deg 19.282 r_lrange_it 6.559 r_lrange_other 6.559 r_dihedral_angle_1_deg 6.343 r_mcangle_it 4.284 r_mcangle_other 4.284 r_scangle_it 4.185 r_scangle_other 4.185
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.144 r_dihedral_angle_3_deg 22.033 r_dihedral_angle_4_deg 19.282 r_lrange_it 6.559 r_lrange_other 6.559 r_dihedral_angle_1_deg 6.343 r_mcangle_it 4.284 r_mcangle_other 4.284 r_scangle_it 4.185 r_scangle_other 4.185 r_mcbond_other 2.541 r_mcbond_it 2.54 r_scbond_it 2.441 r_scbond_other 2.441 r_angle_refined_deg 1.775 r_angle_other_deg 1.763 r_symmetry_nbd_refined 0.298 r_nbd_other 0.297 r_symmetry_nbd_other 0.241 r_nbd_refined 0.223 r_nbtor_refined 0.185 r_xyhbond_nbd_refined 0.155 r_chiral_restr 0.092 r_symmetry_nbtor_other 0.08 r_symmetry_xyhbond_nbd_other 0.018 r_bond_other_d 0.017 r_bond_refined_d 0.013 r_gen_planes_refined 0.009 r_gen_planes_other 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4015 Nucleic Acid Atoms Solvent Atoms 57 Heterogen Atoms 58
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling PHASER phasing