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Neutron and X-ray joint structure of WT-TTR in complex with piceatannol
X-RAY DIFFRACTION - NEUTRON DIFFRACTION
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8W43
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 Disodium malonate, 0.1M NaOAc pH 4.6
Crystal Properties Matthews coefficient Solvent content 1.75 29.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.67 α = 90 b = 85.014 β = 90 c = 65.353 γ = 90
Symmetry Space Group P 21 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 293 PIXEL DECTRIS EIGER X 16M 2022-06-19 M SINGLE WAVELENGTH 2 1 neutron 293 DIFFRACTOMETER iBIX 2022-05-13 L LAUE
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 0.98 Photon Factory BL-17A 2 SPALLATION SOURCE J-PARC MLF BEAMLINE BL-03 2.8-5.7 JPARC MLF BL-03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) R Split (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 1.19 42.51 99.8 0.04 0.016 0.999 23.8 6.3 78555 2 1.9 22.33 98.8 0.153 0.062 0.994 14.9 6.97 19613
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) R Split (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.19 1.23 0.876 0.352 0.774 2.3 2 1.9 1.97 0.646 0.315 0.556 2.7
Refinement Statistics Diffraction ID Structure Solution Method Resolution (High) Resolution (Low) Cut-off Sigma (I) Cut-off Sigma (F) 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 1.19 42.507 1.36 78550 3927 99.77 0.1804 0.1793 0.1802 0.2018 0.2011 NEUTRON DIFFRACTION MOLECULAR REPLACEMENT 1.9 21.784 19579 977 98.87 0.1797 0.1783 0.2064
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 19.121 f_dihedral_angle_d 19.121 f_angle_d 0.917 f_angle_d 0.917 f_chiral_restr 0.096 f_chiral_restr 0.096 f_bond_d 0.029 f_bond_d 0.029 f_plane_restr 0.005 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1771 Nucleic Acid Atoms Solvent Atoms 102 Heterogen Atoms 36