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Co-crystal structure of human transthyretin conjugated to the stilbene substructure derived from reaction with the fluorogenic covalent kinetic stabilizer A2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3TCT Search model was one TTR monomer with ligand removed.
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298 The WT-TTR was concentrated to 4 mg/mL in 10 mM sodium phosphate, 100 mM KCl, at pH 7.6 and co-crystallized at room temperature using the vapor diffusion sitting drop method.
Crystal Properties Matthews coefficient Solvent content 2.12 41.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.96 α = 90 b = 85.201 β = 90 c = 63.751 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 100 PIXEL DECTRIS PILATUS3 2M 2021-12-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 0.97741 ALS 5.0.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) 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 1.5 42.64 95.7 0.029 0.008 1 42.8 12.4 36591 16
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.58 0.411 0.136 0.94 4.9
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 THROUGHOUT 1.5 42.64 34712 1844 95.49 0.16629 0.16483 0.1668 0.19389 0.1952 RANDOM 22.971
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] 0.65 -0.69 0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.671 r_dihedral_angle_3_deg 15.498 r_dihedral_angle_1_deg 14.783 r_dihedral_angle_4_deg 14.571 r_long_range_B_other 8.631 r_long_range_B_refined 8.623 r_scangle_other 6.737 r_scbond_it 4.532 r_scbond_other 4.53 r_mcangle_it 3.701
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.671 r_dihedral_angle_3_deg 15.498 r_dihedral_angle_1_deg 14.783 r_dihedral_angle_4_deg 14.571 r_long_range_B_other 8.631 r_long_range_B_refined 8.623 r_scangle_other 6.737 r_scbond_it 4.532 r_scbond_other 4.53 r_mcangle_it 3.701 r_mcangle_other 3.701 r_angle_refined_deg 2.89 r_mcbond_it 2.559 r_mcbond_other 2.558 r_angle_other_deg 1.604 r_chiral_restr 0.104 r_bond_refined_d 0.046 r_gen_planes_refined 0.013 r_gen_planes_other 0.008 r_bond_other_d 0.004 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 1778 Nucleic Acid Atoms Solvent Atoms 164 Heterogen Atoms 44
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing