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Human transthyretin (TTR) complexed with 3-(9H-fluoren-9-ylideneaminooxy)propanoic acid (inhibitor 15)
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 2.18 43.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.185 α = 90 b = 85.726 β = 90 c = 64.775 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++ 2007-10-11 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 17.61 99.65 23671 23671
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 1.826 100
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 17.61 23671 22457 1214 99.65 0.22769 0.22769 0.22506 0.2709 0.27818 0.3085 RANDOM 32.855
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] 0.5 -0.61 0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.041 r_dihedral_angle_4_deg 23.103 r_dihedral_angle_3_deg 15.138 r_dihedral_angle_1_deg 5.628 r_scangle_it 3.523 r_scbond_it 2.266 r_angle_refined_deg 1.779 r_mcangle_it 1.388 r_mcbond_it 0.838 r_nbtor_refined 0.313
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.041 r_dihedral_angle_4_deg 23.103 r_dihedral_angle_3_deg 15.138 r_dihedral_angle_1_deg 5.628 r_scangle_it 3.523 r_scbond_it 2.266 r_angle_refined_deg 1.779 r_mcangle_it 1.388 r_mcbond_it 0.838 r_nbtor_refined 0.313 r_symmetry_vdw_refined 0.293 r_nbd_refined 0.215 r_symmetry_hbond_refined 0.163 r_xyhbond_nbd_refined 0.151 r_chiral_restr 0.108 r_bond_refined_d 0.014 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1752 Nucleic Acid Atoms Solvent Atoms 181 Heterogen Atoms 40
Software Software Software Name Purpose CrystalClear data collection AMoRE phasing REFMAC refinement CrystalClear data reduction CrystalClear data scaling