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High resolution crystal structure of human transthyretin bound to ligand and conjugates of 3-(5-(3,5-dichloro-4-hydroxyphenyl)-1,3,4-oxadiazol-2-yl)phenyl fluorosulfate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2QGB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 298 The WT-TTR was concentrated to 4 mg/mL in 10 mM NaPi, 100 mM KCl, at pH 7.6 and co-crystallized at room temperature using the vapor-diffusion sitting drop method. Crystals were grown from 1.395 M sodium citrate, 3.5% v/v glycerol at pH 5.5. The crystals were frozen using a cryo-protectant solution of 1.395 M sodium citrate, pH 5.5, containing 10% v/v glycerol
Crystal Properties Matthews coefficient Solvent content 2.27 41.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.709 α = 90 b = 85.42 β = 90 c = 63.537 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 PSI PILATUS 6M 2014-01-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.97945 SSRL BL11-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.25 38.2 99.1 0.029 0.032 0.013 25.5 6.3 64492 64492
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.25 1.32 95.8 0.498 0.498 0.215 1.6 6.2 8993
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 2qgb 1.25 63.54 61174 3263 98.99 0.1471 0.14575 0.1515 0.17232 0.1758 RANDOM 20.421
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] -0.94 0.85 0.08
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 59.37 r_dihedral_angle_2_deg 31.893 r_dihedral_angle_4_deg 19.002 r_dihedral_angle_3_deg 14.08 r_sphericity_bonded 13.42 r_long_range_B_refined 7.438 r_long_range_B_other 7.437 r_rigid_bond_restr 6.56 r_dihedral_angle_1_deg 6.095 r_scangle_other 4.146
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 59.37 r_dihedral_angle_2_deg 31.893 r_dihedral_angle_4_deg 19.002 r_dihedral_angle_3_deg 14.08 r_sphericity_bonded 13.42 r_long_range_B_refined 7.438 r_long_range_B_other 7.437 r_rigid_bond_restr 6.56 r_dihedral_angle_1_deg 6.095 r_scangle_other 4.146 r_scbond_it 3.693 r_scbond_other 3.692 r_angle_other_deg 2.97 r_mcangle_other 2.707 r_mcangle_it 2.692 r_mcbond_it 2.086 r_mcbond_other 2.024 r_angle_refined_deg 1.738 r_chiral_restr 0.101 r_bond_refined_d 0.015 r_gen_planes_other 0.014 r_gen_planes_refined 0.011 r_bond_other_d 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1793 Nucleic Acid Atoms Solvent Atoms 197 Heterogen Atoms 42
Software Software Software Name Purpose REFMAC refinement SCALA data scaling PDB_EXTRACT data extraction