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The determination of the crystal structure of a mutant protein using phases based on a previously determined crystal structure of the wild-type protein is often a straightforward molecular-replacement protocol. Such a structure determination may be difficult if there are large-scale structural differences between the wild-type and mutant proteins. In this manuscript, an interesting case is presented of the unintentional crystallization of a contaminant protein which shared some structural features with the presumed target protein, leading to difficulties in obtaining a completely satisfactory molecular-replacement structure solution. It was not immediately evident that the initial structure solution was incorrect owing to the poor quality of the X-ray diffraction data and low resolution. The structure was subsequently determined by improving the quality of the data and following a sequence-independent MarathonMR protocol. The structure corresponded to that of glycerol dehydrogenase, which crystallized as a contaminant, instead of the presumed mutant of a survival protein encoded by Salmonella typhimurium. The reasons why a solution that appeared to be reasonable was obtained with an incorrect protein model are discussed. The results presented here show that a degree of caution is warranted when handling large-scale structure-determination projects.

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Supplementary Figures S1 and S2.


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S1. SCALA log file obtained from the initial processing of diffraction data which were of lower quality.


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S2. All log files pertaining to the scaling and merging of diffraction data to higher quality.


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S3. The structure of GlyDH determined using the trimmed model of 3-dehydroquinate synthase (PDB entry 3qbd).

PDB reference: glycerol dehydrogenase crystallized as a contaminant, 5wq5

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