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Crystal structure of transthyretin in complex with diflunisal at acidic pH
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4I87
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.6 298 15% (w/v) PEG 2000 monomethylether, 0.1 M ammonium sulfate, 0.05 M sodium acetate buffer, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.16 42.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.8 α = 90 b = 86.22 β = 90 c = 64.32 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 CCD MARMOSAIC 225 mm CCD 2010-08-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.8729 ESRF ID23-2
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 1.69 32.93 99.9 0.06 16.7 6.4 27383 27383
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 1.69 1.78 99.5 0.308 5.2 6.4 3948
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 (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 4I87 1.69 32.93 27383 27111 1365 99.04 0.1915 0.1899 0.189 0.2222 0.2171 random
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] -2.2799 -0.9604 3.2404
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 15.215 f_angle_d 1.222 f_chiral_restr 0.091 f_bond_d 0.009 f_plane_restr 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1781 Nucleic Acid Atoms Solvent Atoms 250 Heterogen Atoms 36
Software Software Software Name Purpose PHENIX refinement MOSFLM data reduction SCALA data scaling