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Crystal Structure of Human Transthyretin in Complex with 2,2',4,4'-tetrahydroxybenzophenone (BP2)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1F41
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.6 291 Purified TTRwt was dialyzed against 10 mM sodiumphosphate buffer with 100 mM KCl pH 7.6 and concentrated to 5 mg per ml. BP2 was added at 5 x molar excess to the protein. The reservoir contained 1.3 to 1.6 M sodium citrate and 3.5 percent
glycerol at pH 5.5. Drop size 3 plus 3 microliter.
Crystal Properties Matthews coefficient Solvent content 2.14 42.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.943 α = 90 b = 85.497 β = 90 c = 64.191 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 PIXEL DECTRIS PILATUS3 6M 2015-02-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.913 ESRF ID29
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 1.45 40 99.4 0.039 23.35 7.1 42623
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.45 1.5 94.9 0.676 2.74 6.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1f41 1.45 38.374 1.34 42619 2147 99.38 0.1332 0.1314 0.1376 0.1677 0.1705
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 14.723 f_angle_d 1.221 f_chiral_restr 0.074 f_bond_d 0.009 f_plane_restr 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1792 Nucleic Acid Atoms Solvent Atoms 240 Heterogen Atoms 43
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing