refine_hand1_rev - Structure Refinement The structure...

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Structure Refinement The structure solution from direct or Patterson methods is frequently already very good. However, the coordinates are not quite accurate, the atom types of some or all atoms have been assigned incorrectly (if at all), and details of the structure are missing (H-atoms, disorders, solvent molecules, etc .). The atomic positions in the first solution are not the direct result of the diffraction experiment, but an interpretation of the electron density function calculated from the measured intensities and the “somehow determined” phase angles. Better phases can be calculated from the atomic positions, which allow re-determining of the electron density function with a higher precision. From the new electron density map, more accurate atomic positions can be derived, which lead to even better phase angles, and so forth. In every such cycle, adjustments to the atomic model are made: atom types are changed, missing atoms are introduced, etc. This whole process is called structure refinement.
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Structure Refinement: Three Main Steps Close examination of the F o - F c map helps to introduce new atoms and remove “bad” old ones. Once all non-hydrogen atoms are found, the atoms can be refined anisotropically. Once the model is anisotropic, the hydrogen atom positions can be determined or calculated.
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Structure Refinement: Electron Density Maps Different electron density maps: F o map : Electron density calculated using observed structure factures combined with phases calculated from the atomic model. This map shows the observed electron density; its accuracy depends largely on the accuracy of the phases. F c map : Electron density calculated from structure factors and phases calculated from the atomic model. This map shows the electron density according to the model only. F o - F c map : The difference between the two maps. Has close-to-zero values for parts of the model that are consistent with the experimental density, large positive values at places where the model should have an atom, but does not, and large negative values at places where the model has an atom, which should not be there. Weaker positive or negative values for the F o - F c map could point to wrongly assigned atom types.
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Structure Refinement: Electron Density Maps F o map Model: A Cp ring F o - F c map Examination of the electron density maps shows that ligand in the current model is not a Cp ring, but in fact a Cp* ring.
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Structure Refinement: Anisotropic Displacement Parameters It is reasonable to assume that atoms move anisotropically, i.e. with different amplitudes in different directions. Instead of describing an atom as a sphere, it is described as an ellipsoid; the elements of the matrix describing the ellipsoid are called anisotropic displacement parameters (ADP):
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Structure Refinement: Anisotropic Displacement Parameters The size of the ellipsoids (or spheres in the isotropic case) is chosen so that the ellipsoid includes 50% electron density of the atom type in the
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refine_hand1_rev - Structure Refinement The structure...

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