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High resolution crystal structure of human transthyretin bound to ligand and conjugates of 4-(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 with inhibitors 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, vapor diffusion, sitting drop, temperature 298.0
Crystal Properties Matthews coefficient Solvent content 2.33 42.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.093 α = 90 b = 85.522 β = 90 c = 64.65 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 2013-11-22 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 1.349 38.484 99.5 0.028 0.031 0.012 28.4 6.4 53165 53165 14.6
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 1.35 1.42 98 0.449 0.449 0.194 1.6 6.2 7514
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 1.35 38.484 50399 2693 99.4 0.1591 0.1574 0.1571 0.1951 0.1957 RANDOM 21.614
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] 0.13 -0.32 0.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.791 r_sphericity_free 20.602 r_dihedral_angle_4_deg 15.481 r_dihedral_angle_3_deg 13.769 r_sphericity_bonded 8.128 r_dihedral_angle_1_deg 5.935 r_rigid_bond_restr 3.012 r_mcangle_it 2.417 r_mcbond_it 2.092 r_mcbond_other 2.013
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.791 r_sphericity_free 20.602 r_dihedral_angle_4_deg 15.481 r_dihedral_angle_3_deg 13.769 r_sphericity_bonded 8.128 r_dihedral_angle_1_deg 5.935 r_rigid_bond_restr 3.012 r_mcangle_it 2.417 r_mcbond_it 2.092 r_mcbond_other 2.013 r_angle_refined_deg 1.694 r_angle_other_deg 1.361 r_chiral_restr 0.082 r_bond_refined_d 0.015 r_gen_planes_refined 0.009 r_gen_planes_other 0.006 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1789 Nucleic Acid Atoms Solvent Atoms 156 Heterogen Atoms 96
Software Software Software Name Purpose SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data scaling XDS data reduction