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The solvent-picking procedure in phenix.refine has been extended and combined with Phaser anomalous substructure completion and analysis of coordination geometry to identify and place elemental ions.
Keywords: refinement; ions; PHENIX.

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The crystal structure of arabinose-5-phosphate isomerase from B. fragilis NCTC 9343 in complex with an endogenous ligand, CMP-Kdo, is described. Structural and sequence comparisons suggest highly conserved functional residues in the active site that could be targeted for antibacterial drug design.
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