I should like to point out here that almost ANY protein will pick
up something from the crystallization solution (cations, anions).
Unfortunately, in the majority of cases these partially occupied
ions will not be seen or will be mistakenly interpreted as water
molecules. One way to 'see' such things is to carefully inspect
an anomalous difference Fourier electron density map from good
quality data collected at longer wavelength (even CuKa is good
enough for that.
See: Mueller-Dieckmann et al (2007). Acta Cryst D63, 366-380.
A most spectacular example is the recent PDB entry 2RKP, where
at least 16 chlorides have been identified based on a data set
collected at a wavelength of 2.0 A.
Cheers, Manfred.
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