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In order to solve the structure of a protein by x-ray crystallography, a biochemist must first find the conditions in which the protein is able to be crystallized. Some proteins have natively unstructured regions ("floppy parts") that make the protein unable to be crystallized. Many times, the protein will be recombinantly expressed without these unstructured regions, and the positions of these residues will not be found. Other times, the positions will not be found because there are too many alternate positions in the crystal and the locations of the residues will not be found in the electron density.

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Q: Why do some x-ray crystallographic protein structures omit some amino acids?
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