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Human transthyretin (TTR) complexed with (S)-3-(9H-fluoren-9-ylideneaminooxy)-2-methylpropanoic acid (inhibitor 16)
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 2.2 44.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.39 α = 90 b = 85.979 β = 90 c = 65.076 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 2007-02-02 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 1.85 19.37 98.69 21224 21224
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.85 1.898 97.45
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 1.85 19.37 21224 20135 1089 98.69 0.23165 0.23165 0.22964 0.2292 0.2693 0.2702 RANDOM 38.768
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] 1.58 -1.46 -0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.967 r_dihedral_angle_3_deg 19.289 r_dihedral_angle_4_deg 18.864 r_dihedral_angle_1_deg 6.487 r_scangle_it 4.954 r_scbond_it 3.316 r_mcangle_it 2.276 r_angle_refined_deg 2.227 r_mcbond_it 1.504 r_nbtor_refined 0.317
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.967 r_dihedral_angle_3_deg 19.289 r_dihedral_angle_4_deg 18.864 r_dihedral_angle_1_deg 6.487 r_scangle_it 4.954 r_scbond_it 3.316 r_mcangle_it 2.276 r_angle_refined_deg 2.227 r_mcbond_it 1.504 r_nbtor_refined 0.317 r_symmetry_vdw_refined 0.269 r_nbd_refined 0.218 r_xyhbond_nbd_refined 0.149 r_chiral_restr 0.137 r_symmetry_hbond_refined 0.136 r_bond_refined_d 0.023 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1731 Nucleic Acid Atoms Solvent Atoms 138 Heterogen Atoms 42
Software Software Software Name Purpose CrystalClear data collection AMoRE phasing REFMAC refinement CrystalClear data reduction CrystalClear data scaling