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Human Transthyretin (TTR) Complexed with Hydroxylated polychlorinated Biphenyl-4-hydroxy-2',3,3',4',5-Pentachlorobiphenyl
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 CRYSTALLIZATION CONDITIONS: 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 2.14 42.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.081 α = 90 b = 85.461 β = 90 c = 64.237 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 1999-07-31 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 1.85 27.42 90.5 0.036 18746 18746
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 1.85 1.898 87.52
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 1.85 27.42 18746 17787 959 89.65 0.21586 0.21586 0.21375 0.25745 RANDOM 29.503
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] 0.62 -0.3 -0.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.347 r_dihedral_angle_3_deg 14.8 r_dihedral_angle_4_deg 14.689 r_dihedral_angle_1_deg 5.593 r_scangle_it 3.924 r_scbond_it 2.646 r_mcangle_it 1.823 r_angle_refined_deg 1.496 r_mcbond_it 1.253 r_symmetry_hbond_refined 0.796
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.347 r_dihedral_angle_3_deg 14.8 r_dihedral_angle_4_deg 14.689 r_dihedral_angle_1_deg 5.593 r_scangle_it 3.924 r_scbond_it 2.646 r_mcangle_it 1.823 r_angle_refined_deg 1.496 r_mcbond_it 1.253 r_symmetry_hbond_refined 0.796 r_nbtor_refined 0.324 r_nbd_refined 0.238 r_symmetry_vdw_refined 0.229 r_xyhbond_nbd_refined 0.17 r_chiral_restr 0.085 r_gen_planes_refined 0.035 r_bond_refined_d 0.011 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 1770 Nucleic Acid Atoms Solvent Atoms 51 Heterogen Atoms 36
Software Software Software Name Purpose HKL-2000 data collection SCALEPACK data scaling AMoRE phasing REFMAC refinement HKL-2000 data reduction