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Human transthyretin (TTR) complexed with (E)-3-(2-methoxybenzylideneaminooxy)propanoic acid (inhibitor 13)
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 7 290 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. All TTR:ligand complexes were prepared from crystals soaked with a ten fold molar excess of ligand for more than three weeks.
, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal Properties Matthews coefficient Solvent content 2.07 40.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.169 α = 90 b = 84.757 β = 90 c = 63.807 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 2008-01-16 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 1.8 20.11 98.96 21648 21648
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.8 1.847 93.97
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 1.8 20.11 21668 20553 1115 98.96 0.22685 0.22685 0.22471 0.2242 0.26581 0.2725 RANDOM 40.261
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] 0.44 -1.38 0.95
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.942 r_dihedral_angle_3_deg 17.126 r_dihedral_angle_4_deg 6.548 r_dihedral_angle_1_deg 6.034 r_scangle_it 5.127 r_scbond_it 3.374 r_mcangle_it 2.404 r_angle_refined_deg 1.924 r_mcbond_it 1.502 r_nbtor_refined 0.319
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.942 r_dihedral_angle_3_deg 17.126 r_dihedral_angle_4_deg 6.548 r_dihedral_angle_1_deg 6.034 r_scangle_it 5.127 r_scbond_it 3.374 r_mcangle_it 2.404 r_angle_refined_deg 1.924 r_mcbond_it 1.502 r_nbtor_refined 0.319 r_nbd_refined 0.224 r_symmetry_vdw_refined 0.211 r_symmetry_hbond_refined 0.146 r_xyhbond_nbd_refined 0.144 r_chiral_restr 0.127 r_bond_refined_d 0.019 r_gen_planes_refined 0.008 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1731 Nucleic Acid Atoms Solvent Atoms 143 Heterogen Atoms 32
Software Software Software Name Purpose CrystalClear data collection AMoRE phasing REFMAC refinement CrystalClear data reduction CrystalClear data scaling