Hello,
a really molecule should show up also in the 2Fo-Fc type map. This appears not to be the case.
So indeed it is likely that your density corresponds to some alternate conformation of the surrounding residues present with low occupancy. The glutamic acid sidechain could be modelled, but I have some doubts about the rest.
If the refinement is almost finished, it could simply be noise.
Best
Wim

On 03/07/2018 04:23, Uma Gabale wrote:

Dear all,

We came across a blob of unidentified electron density in a shallow cavity of a bacterial protein structure (pictures attached). It is surrounded by residues Asp, Arg, Gln, His, Glu, Thr, and Trp.

The protein was expressed in E. coli BL21(DE3) and purified on Ni-NTA followed by gel filtration. The purification buffers included Tris, crystallization condition had HEPES and PEG3350; perfluoropolyether was used as a cryoprotectant.

We would appreciate any help in identifying it.​

Thanks and regards,

Uma.

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Uma Gabale, PhD

Research Associate

Molecular and Cellular Biochemistry
Indiana University Bloomington

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Wim Burmeister
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Institut de Biologie Structurale (IBS) CIBB
71 avenue des Martyrs

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