Solving the phase problem experimentally
This chapter covers methods of structure solution which are used when molecular replacement is impossible, usually due to the lack of a suitable search model. These methods require that additional atoms are introduced into the protein, either by soaking the crystal or by special expression methods. These atoms are chosen to perturb the diffraction pattern of the protein which, firstly, allows the positions of the added atoms to be determined and, secondly, allows the phases of the protein molecule to be calculated. Methods for analysing the data from such derivatives are covered in detail as are methods for locating the additive atoms and refining their positions, many of which rely on the Patterson function. The chapter then introduces the theory of calculating the phases of the protein and treatment of the associated errors. The important role which anomalous scattering, most notably that of selenomethionine, plays in phasing is described in detail along with the associated theory. Density modification methods for improving the accuracy of the resulting phases are then covered.
Keywords: isomorphism, heavy atom derivatives, scaling, Patterson function, Patterson solution, cross-phasing, multiple-isomorphous replacement, phasing diagram, phase calculation, density modification
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