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Kinetic Stabilization of transthyretin through covalent modification of K15 by 3-(5-(3,5-dichloro-4-hydroxyphenyl)-1,3,4-oxadiazol-2-yl)-benzenesulfonamide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2FBR PDB ENTRY 2FBR
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, VAPOR DIFFUSION, SITTING DROP
Crystal Properties Matthews coefficient Solvent content 2.11 41.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.968 α = 90 b = 85.757 β = 90 c = 63.193 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 Rh coated flat mirror 2012-04-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 0.9795 SSRL BL12-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) 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 1.4 85.76 99.2 0.076 12.2 5.8 46117 21
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.4 1.45 99.5 0.548 5.9 4552
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 PDB ENTRY 2FBR 1.402 85.76 45953 2315 98.67 0.1707 0.1689 0.1682 0.2052 0.2017 RANDOM 24.0679
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] -0.4 -1.16 1.56
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.215 r_dihedral_angle_4_deg 22.346 r_dihedral_angle_3_deg 14.949 r_scangle_it 6.951 r_dihedral_angle_1_deg 6.036 r_scbond_it 4.692 r_mcangle_it 3.536 r_mcbond_it 2.185 r_rigid_bond_restr 1.852 r_angle_refined_deg 1.684
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.215 r_dihedral_angle_4_deg 22.346 r_dihedral_angle_3_deg 14.949 r_scangle_it 6.951 r_dihedral_angle_1_deg 6.036 r_scbond_it 4.692 r_mcangle_it 3.536 r_mcbond_it 2.185 r_rigid_bond_restr 1.852 r_angle_refined_deg 1.684 r_angle_other_deg 0.945 r_mcbond_other 0.624 r_chiral_restr 0.114 r_bond_refined_d 0.017 r_gen_planes_refined 0.009 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1785 Nucleic Acid Atoms Solvent Atoms 142 Heterogen Atoms 46
Software Software Software Name Purpose SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling