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High Resolution Structure of Wild Type Human Transthyretin in Complex with 3,3',5,5'-tetrachloro-[1,1'-biphenyl]-4,4'diol
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2FBR PDB ENTRY 2FBR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 298 4 mg/ML wt-TTR in 10 mM sodium phosphate, 100 mM potassium chloride, pH 7.6, co-crystallized with inhibitor, crystallization solution: 1.395 M sodium citrate, 3.5% v/v glycerol, pH 5.5, cryoprotectant: 1.395 M sodium citrate, pH 5.5, 10% v/v glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.15 42.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.049 α = 90 b = 85.02 β = 90 c = 64.893 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 200 PIXEL DECTRIS PILATUS 6M Rh coated flat mirror 2013-07-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.9797 SSRL BL11-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.22 35.873 99.5 0.028 27.6 6.3 70897 13.9
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.22 1.29 98.2 0.515 3.5 6 10085
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 (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 2FBR 1.22 35.873 67215 3580 99.25 0.15168 0.15053 0.1528 0.17339 0.1753 RANDOM 17.368
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] -0.04 -0.02 0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.931 r_sphericity_free 30.197 r_dihedral_angle_4_deg 18.792 r_sphericity_bonded 13.687 r_dihedral_angle_3_deg 11.602 r_dihedral_angle_1_deg 6.292 r_rigid_bond_restr 4.684 r_angle_refined_deg 1.649 r_angle_other_deg 0.952 r_chiral_restr 0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.931 r_sphericity_free 30.197 r_dihedral_angle_4_deg 18.792 r_sphericity_bonded 13.687 r_dihedral_angle_3_deg 11.602 r_dihedral_angle_1_deg 6.292 r_rigid_bond_restr 4.684 r_angle_refined_deg 1.649 r_angle_other_deg 0.952 r_chiral_restr 0.1 r_bond_refined_d 0.015 r_gen_planes_refined 0.009 r_gen_planes_other 0.002 r_bond_other_d 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1782 Nucleic Acid Atoms Solvent Atoms 179 Heterogen Atoms 36
Software Software Software Name Purpose autoXDS data collection PHASER phasing REFMAC refinement autoXDS data reduction autoXDS data scaling