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Human Transthyretin (TTR) Complexed with Hydroxylated polychlorinated Biphenyl-4,4'-dihydroxy-3,3',5,5'-tetrachlorobiphenyl
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1BMZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 298 Crystals of recombinant WT TTR were obtained from protein solutions at 5 mg/ml (in 100 mM KCl, 100 mM phosphate [pH 7.4], 1 M ammonium sulfate) equilibrated against 2 M ammonium sulfate in hanging drop experiments. The TTR ligand complexes were prepared from crystals soaked for 2 weeks with a 10-fold molar excess , pH 7.00, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.18 43.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.239 α = 90 b = 85.841 β = 90 c = 64.793 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 MAC Science DIP-2030 1999-06-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 27.52 92.1 0.037 21209 21209
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 1.8 1.86 92.4
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-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1BMZ 1.8 27.52 21209 21209 1097 92.07 0.18199 0.18199 0.17998 0.21972 RANDOM 24.923
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] 0.75 -0.29 -0.46
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.303 r_dihedral_angle_4_deg 17.212 r_dihedral_angle_3_deg 14.674 r_dihedral_angle_1_deg 5.365 r_scangle_it 5.283 r_scbond_it 3.516 r_mcangle_it 2.124 r_angle_refined_deg 1.497 r_mcbond_it 1.466 r_nbtor_refined 0.313
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.303 r_dihedral_angle_4_deg 17.212 r_dihedral_angle_3_deg 14.674 r_dihedral_angle_1_deg 5.365 r_scangle_it 5.283 r_scbond_it 3.516 r_mcangle_it 2.124 r_angle_refined_deg 1.497 r_mcbond_it 1.466 r_nbtor_refined 0.313 r_symmetry_hbond_refined 0.311 r_symmetry_vdw_refined 0.26 r_nbd_refined 0.218 r_xyhbond_nbd_refined 0.2 r_chiral_restr 0.104 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 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 1750 Nucleic Acid Atoms Solvent Atoms 120 Heterogen Atoms 36
Software Software Software Name Purpose SCALEPACK data scaling AMoRE phasing REFMAC refinement HKL-2000 data reduction