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Kinetic stabilization of transthyretin through covalent modification of K15 by (E)-N-(4-(4-hydroxy-3,5-dimethylstyryl)phenyl)propionamide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 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 298K
Crystal Properties Matthews coefficient Solvent content 2.13 42.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.966 α = 90 b = 85.157 β = 90 c = 64.132 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 PIXEL PSI PILATUS 6M Rh coated flat mirror 2012-04-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.9795 SSRL BL11-1
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 1.45 85.16 99.9 0.044 55.9 8.2 42818 20.4
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.45 1.5 100 0.519 3.7 8.1 4221
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 2FBR 1.45 85.16 42350 2139 99.56 0.1665 0.1654 0.1647 0.1873 0.1923 RANDOM 23.2489
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] 0.6 -0.36 -0.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.154 r_dihedral_angle_4_deg 20.317 r_dihedral_angle_3_deg 14.591 r_scangle_it 7.076 r_dihedral_angle_1_deg 6.211 r_scbond_it 4.696 r_mcangle_it 3.596 r_mcbond_it 2.198 r_rigid_bond_restr 1.904 r_angle_refined_deg 1.727
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.154 r_dihedral_angle_4_deg 20.317 r_dihedral_angle_3_deg 14.591 r_scangle_it 7.076 r_dihedral_angle_1_deg 6.211 r_scbond_it 4.696 r_mcangle_it 3.596 r_mcbond_it 2.198 r_rigid_bond_restr 1.904 r_angle_refined_deg 1.727 r_angle_other_deg 0.954 r_mcbond_other 0.619 r_chiral_restr 0.109 r_bond_refined_d 0.017 r_gen_planes_refined 0.01 r_gen_planes_other 0.005 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1785 Nucleic Acid Atoms Solvent Atoms 82 Heterogen Atoms 44
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction