However, treatment with urea is known to modify proteins (N-term/Lys/Arg), which could ultimately effect crystallization.

Is this something that people generally worry about?
For example
-would you bother cleaning up the urea by ion exchange
-get ultra pure urea (ultra $$$)
-change to guanidinium chloride
-hope that it might benefit crystallization (i.e. similar to methylation of lysines)

Have ~ 50 mM glycine or tris in your urea solution and prepare it fresh. Then you don't have to worry about carbamylation.

Dima

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