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Human Transthyretin (TTR) Complexed with Hydroxylated polychlorinated Biphenyl-4-hydroxy-3,3',5,4'-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 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 , VAPOR DIFFUSION, HANGING DROP
Crystal Properties Matthews coefficient Solvent content 2.22 44.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.459 α = 90 b = 86.197 β = 90 c = 65.488 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 1999-07-14 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 65.51 89.2 0.03 19133 19133
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 92.35
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 65.51 19133 18145 988 88.22 0.21147 0.21147 0.21008 0.23769 RANDOM 23.974
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] 0.12 0.03 -0.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.822 r_dihedral_angle_4_deg 26.403 r_dihedral_angle_3_deg 14.456 r_dihedral_angle_1_deg 5.676 r_scangle_it 5.293 r_scbond_it 3.26 r_angle_refined_deg 2.272 r_mcangle_it 2.105 r_mcbond_it 1.101 r_nbtor_refined 0.311
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.822 r_dihedral_angle_4_deg 26.403 r_dihedral_angle_3_deg 14.456 r_dihedral_angle_1_deg 5.676 r_scangle_it 5.293 r_scbond_it 3.26 r_angle_refined_deg 2.272 r_mcangle_it 2.105 r_mcbond_it 1.101 r_nbtor_refined 0.311 r_nbd_refined 0.194 r_symmetry_vdw_refined 0.179 r_xyhbond_nbd_refined 0.109 r_chiral_restr 0.107 r_symmetry_hbond_refined 0.102 r_gen_planes_refined 0.065 r_bond_refined_d 0.016 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 1731 Nucleic Acid Atoms Solvent Atoms 75 Heterogen Atoms 34
Software Software Software Name Purpose HKL-2000 data collection SCALEPACK data scaling AMoRE phasing REFMAC refinement HKL-2000 data reduction