☰ Navigation Tabs
Kinetic Stabilization of transthyretin through covalent modification of K15 by 4-bromo-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 2.15 42.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.185 α = 90 b = 86.143 β = 90 c = 63.693 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 2011-06-24 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 1.22 86.143 99.2 0.079 10.7 5.7 70853 16.9
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 1.22 1.26 99.6 0.647 4.8 7022
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 1.22 86.14 70648 3577 98.89 0.1691 0.1676 0.169 0.1966 0.195 RANDOM 21.2477
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] 0.5 -0.68 0.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.375 r_dihedral_angle_4_deg 14.731 r_dihedral_angle_3_deg 14.052 r_scangle_it 7.17 r_dihedral_angle_1_deg 6.238 r_scbond_it 4.801 r_mcangle_it 3.648 r_mcbond_it 2.307 r_rigid_bond_restr 1.925 r_angle_refined_deg 1.771
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.375 r_dihedral_angle_4_deg 14.731 r_dihedral_angle_3_deg 14.052 r_scangle_it 7.17 r_dihedral_angle_1_deg 6.238 r_scbond_it 4.801 r_mcangle_it 3.648 r_mcbond_it 2.307 r_rigid_bond_restr 1.925 r_angle_refined_deg 1.771 r_angle_other_deg 0.973 r_mcbond_other 0.687 r_chiral_restr 0.109 r_bond_refined_d 0.018 r_gen_planes_refined 0.01 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1781 Nucleic Acid Atoms Solvent Atoms 143 Heterogen Atoms 48
Software Software Software Name Purpose SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction DENZO data reduction