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Human TTR altered by a rhenium tris-carbonyl Pyta-C12 derivative
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5K1J
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 293 protein: 10 mg/ml Dialysed in 100 milli-M NaCl, 50 milli-M sodium acetate, pH 5.5
precipitant: 21% polyethylene glycol 4,000 (PEG4K), 0.14 M imidazole malate, pH 6.0 + 3.6% polyethylene glycol monomethyl ether (MPEG5K), 30 mM sodium
acetate pH 5.5
cryosoak: 40% SM3 (25 % diethylene glycol + 25 % ethylene glycol + 25 % glycerol + 25 % 1,4-dioxane) 50% PEG 8K and 0.5 milli-M of rhenium tris-carbonyl Pyta-C12 derivative.
Crystal Properties Matthews coefficient Solvent content 2.29 46.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.65 α = 90 b = 82.13 β = 90 c = 67.72 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 EIGER X 9M mirrors 2016-04-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 2 1.175919 SOLEIL PROXIMA 2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) CC (Half) 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 1.81 50 98.2 0.065 0.052 0.998 12.31 2.6 41147 -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 1.81 1.86 98.4 0.782 1.69 2.6
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 THROUGHOUT 5K1J 1.81 41.065 1.26 41116 2050 98.1 0.1906 0.1888 0.1936 0.2239 0.23
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 18.269 f_angle_d 0.819 f_chiral_restr 0.056 f_plane_restr 0.006 f_bond_d 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1785 Nucleic Acid Atoms Solvent Atoms 154 Heterogen Atoms 31
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling REFMAC phasing