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A novel chemical derivative(89) of THRB agonist
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 0.1 M MgSO4 and 12% PEG 6000.
Crystal Properties Matthews coefficient Solvent content 2.61 52.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 106.234 α = 90 b = 106.234 β = 90 c = 56.866 γ = 90
Symmetry Space Group P 43 21 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 SSRF BL19U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.57 50 100 0.096 0.101 0.03 7.6 12.2 10838
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 2.57 2.61 100 1.482 1.551 0.453 0.609 11.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 THROUGHOUT 6KKB 2.57 47.55 9793 499 95.29 0.2175 0.2152 0.2163 0.261 0.2533 RANDOM 47.174
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] -0.57 -0.57 1.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.991 r_dihedral_angle_4_deg 19.144 r_dihedral_angle_3_deg 15.514 r_dihedral_angle_1_deg 5.319 r_angle_refined_deg 1.457 r_angle_other_deg 1.375 r_chiral_restr 0.075 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_gen_planes_other 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.991 r_dihedral_angle_4_deg 19.144 r_dihedral_angle_3_deg 15.514 r_dihedral_angle_1_deg 5.319 r_angle_refined_deg 1.457 r_angle_other_deg 1.375 r_chiral_restr 0.075 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1950 Nucleic Acid Atoms Solvent Atoms 47 Heterogen Atoms 38
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling PDB_EXTRACT data extraction HKL-2000 data reduction PHASER phasing