Have you done both experiments at the same temperature? If cryo - have you used the same cryoprotectant?
same ionic strength? Did mutations cause changes in the surface charge distribution/hydrophobic/hydrophilic/ pi...pi interactions - if yes how it can effect quaternary structure of native. Do mutations in the model of that crystal and take a close look at the interfaces
Look at Acta Cryst. 2006, D62, 766- to see discussion about effect of freezing
In general if it is an external flexible loop I would be neither surprised nor worried, if different in the "rigid" core you need to seek explanation. Withdrawal/addition of water molecules causing tautomeric changes in Pro (from trans to cis peptide?) and as a result a shift of some fragment? It is known to happen and can move a domain.
Good luck - ESJ
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Dr. Ewa Skrzypczak-Jankun Associate Professor
Department of Urology Dowling Hall r. 2257
3000 Arlington Ave. phone 419 383 5414
Toledo OH 43614 fax 419 383 3785
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