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Human transthyretin (TTR) complexed with bivalant amyloid inhibitor (4 carbon linker)
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 TTR bivalent inhibitor complexes of 1:1 stoichiometry resulting from coassembly at 5-7 mg/mL (95-133 microM in 100 mM KCl, 1 mM EDTA, 10 mM sodium phosphate, 0.35-0.50 M ammonium sulfate equilibrated against 2 M ammonium sulfate, pH 7.00, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.14 42.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.599 α = 90 b = 84.355 β = 90 c = 65.569 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 100 CCD SBC-3 2002-11-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM 0.97918 APS 19-BM
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 1.46 42.26 97.73 38794 38794 38794
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 1.46 1.498 94
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 (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1BMZ 1.46 42.26 38794 2062 97.73 0.21076 0.21076 0.21005 0.22356 RANDOM 17.399
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] -0.77 0.11 0.65
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.225 r_scangle_it 4.851 r_scbond_it 3.01 r_mcangle_it 2.167 r_angle_refined_deg 1.721 r_angle_other_deg 1.488 r_mcbond_it 1.196 r_symmetry_vdw_other 0.306 r_nbd_other 0.267 r_nbd_refined 0.198
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.225 r_scangle_it 4.851 r_scbond_it 3.01 r_mcangle_it 2.167 r_angle_refined_deg 1.721 r_angle_other_deg 1.488 r_mcbond_it 1.196 r_symmetry_vdw_other 0.306 r_nbd_other 0.267 r_nbd_refined 0.198 r_xyhbond_nbd_refined 0.161 r_symmetry_hbond_refined 0.146 r_symmetry_vdw_refined 0.129 r_chiral_restr 0.126 r_nbtor_other 0.087 r_bond_refined_d 0.018 r_bond_other_d 0.014 r_gen_planes_refined 0.01 r_gen_planes_other 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1770 Nucleic Acid Atoms Solvent Atoms 181 Heterogen Atoms 37
Software Software Software Name Purpose SCALEPACK data scaling AMoRE phasing REFMAC refinement HKL-2000 data reduction EPMR phasing