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Figure 4
Examples of ion placement using the JCSG data, illustrating potential pitfalls. The models are taken from the PDB, but with maps calculated after attempting to replace the ions in phenix.refine. Colors are as in Fig. 3[link]; anomalous maps are shown in all cases, but signal may be below the contour level. Where shown, purple sticks represent a symmetry-related molecule. Sites shown in (a), (b) and (e) were placed successfully; for (b) and (c) the originally built atoms are shown for clarity. (a) Native Zn sites in 3lub. (b) Nonspecific Ca sites in 3lub built and refined as waters by phenix.refine. (c) Ambiguous sites in 4ecg originally built as Ca2+. (d) New Ca2+ site in 3cjy. (e) New Zn2+ site in 3h50 (Axelrod et al., 2010BB6).

Journal logoSTRUCTURAL
BIOLOGY
ISSN: 2059-7983
Volume 70| Part 4| April 2014| Pages 1104-1114
https://doi.org/10.1107/S1399004714001308
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