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Human transthyretin (TTR) complexed with 16-alpha-bromo-estradiol
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3GS4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.2 293 Protein: 5 mg/ml TTR dialysed against 0.1 M NaCl, 0.05M Na acetate, pH 5.5.
Precipitant:: 70% (30% PEG 4000, 0.2M imidazole malate, pH 6.0) 30% (18% monomethyl PEG 2000, 0.1 M sodium cacodylate, pH 6.5).
Cryoprotectant: 40% (25 % diethylene glycol + 12.5 % MPD + 37.5 % 2,3-butanediol + 12.5 % 1,4-dioxane) 50% (12.5% MPEG 5K, 25% MPEG 550) 0.1 M (mixed Na propionate, Na cacodylate, Bis-Tris-propane 50% at pH 4.0 and 50% pH 9.5)
Crystal Properties Matthews coefficient Solvent content 2.14 42.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.202 α = 90 b = 86.134 β = 90 c = 63.395 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 PILATUS 6M 2014-01-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.87 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.23 43.067 98 0.118 0.111 11.73 9.32 69505 68116 -3
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 1.23 1.27 96.4 1.22 1.88 9.58
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3GS4 1.23 43.067 1.34 68063 3416 98 0.1784 0.1767 0.1776 0.2106 0.211 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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 16.062 f_angle_d 1.304 f_chiral_restr 0.05 f_bond_d 0.007 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1794 Nucleic Acid Atoms Solvent Atoms 334 Heterogen Atoms 50
Software Software Software Name Purpose PHENIX refinement REFMAC refinement Coot model building XDS data scaling XSCALE data scaling ADSC data collection