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Human Transthyretin (TTR) complexed with(E)-3-(2-(trifluoromethyl)benzylideneaminooxy)propanoic acid (inhibitor 11)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1BMZ PDB entry 1BMZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 289 Crystals of wt-TTR were obtained from 5-7 mg/mL protein solutions (in 100 mM KCl, 1 mM EDTA, 10 mM sodium phosphate, pH 7.0, 0.3 M ammonium sulfate) equilibrated against 2 M ammonium sulfate in hanging drops. TTR:ligand complexes were prepared from crystals soaked with a tenfold molar excess of ligand for more than two weeks., VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.06 40.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.181 α = 90 b = 84.939 β = 90 c = 63.422 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 120 IMAGE PLATE RIGAKU RAXIS IV++ mirrors 2007-02-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.78 63.37 99.71 22460 22460
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.78 1.826 99.94
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 1BMZ 1.78 18.45 22460 22460 1149 99.71 0.22668 0.22668 0.22417 0.276 0.27349 0.323 RANDOM 31.604
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] 0.47 -0.62 0.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.839 r_dihedral_angle_4_deg 21.177 r_dihedral_angle_3_deg 16.396 r_dihedral_angle_1_deg 5.942 r_scangle_it 3.223 r_scbond_it 2.42 r_angle_refined_deg 1.759 r_mcangle_it 1.313 r_mcbond_it 0.877 r_nbtor_refined 0.313
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.839 r_dihedral_angle_4_deg 21.177 r_dihedral_angle_3_deg 16.396 r_dihedral_angle_1_deg 5.942 r_scangle_it 3.223 r_scbond_it 2.42 r_angle_refined_deg 1.759 r_mcangle_it 1.313 r_mcbond_it 0.877 r_nbtor_refined 0.313 r_symmetry_vdw_refined 0.235 r_nbd_refined 0.21 r_xyhbond_nbd_refined 0.137 r_symmetry_hbond_refined 0.111 r_chiral_restr 0.105 r_bond_refined_d 0.016 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1709 Nucleic Acid Atoms Solvent Atoms 158 Heterogen Atoms 36
Software Software Software Name Purpose CrystalClear data collection AMoRE phasing REFMAC refinement CrystalClear data reduction CrystalClear data scaling