☰ Navigation Tabs
Transthyretin in complex with the fluorescent folding sensor (E)-7-hydroxy-3-(4-hydroxy-3,5-dimethylstyryl)-4-methyl-2H-chromen-2-one
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 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 298.0K
Crystal Properties Matthews coefficient Solvent content 2.11 41.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.793 α = 90 b = 85.646 β = 90 c = 63.562 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 200 PIXEL DECTRIS PILATUS 6M Mirrors 2012-07-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.9797 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 1.13 38.28 98.5 0.021 34.3 6.1 87639 10.2
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 1.13 1.19 90.7 0.34 4.9 57501
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 1.13 38.28 87538 4383 98.37 0.1616 0.1609 0.1616 0.1743 0.1729 RANDOM 16.7933
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] -0.26 -0.08 0.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.425 r_dihedral_angle_4_deg 19.378 r_dihedral_angle_3_deg 14.104 r_sphericity_free 7.929 r_dihedral_angle_1_deg 6.209 r_scangle_it 5.002 r_sphericity_bonded 4.86 r_scbond_it 3.374 r_mcangle_it 2.922 r_mcbond_it 1.874
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.425 r_dihedral_angle_4_deg 19.378 r_dihedral_angle_3_deg 14.104 r_sphericity_free 7.929 r_dihedral_angle_1_deg 6.209 r_scangle_it 5.002 r_sphericity_bonded 4.86 r_scbond_it 3.374 r_mcangle_it 2.922 r_mcbond_it 1.874 r_angle_refined_deg 1.705 r_rigid_bond_restr 1.594 r_angle_other_deg 0.943 r_mcbond_other 0.77 r_chiral_restr 0.104 r_bond_refined_d 0.015 r_gen_planes_refined 0.009 r_bond_other_d 0.006 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1783 Nucleic Acid Atoms Solvent Atoms 250 Heterogen Atoms 48
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction Blu-Ice data collection PHASER phasing