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Solvent flattening of macromolecular MIR electron density maps is frequently used to improve the quality of the phases and the interpretability of resultant electron density maps. A new method is presented by which the heavy-atom parameters of isomorphous derivatives are refined against these same solvent-flattened phases and is shown to enhance convergence of the parameters by decoupling heavy-atom-parameter adjustment from parent-phase calculation. This approach is described here in the first example of its application in the solution of the glutaminyl-tRNA synthetase-tRNAGln-ATP co-crystal structure.
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