extra density ??

From: stacy William
Date: 19 January 2012 06:44

Dear All, 

 I am working on plant proteins and solved a structure, there is an extra density which i cannot fix . I am attaching the coot image , can anybody suggest me what it could be

THANKS :)

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From: Antony Oliver


Stacy,

It looks like it's just some noise on your two-fold symmetry axis.
You could probably model some/most of it with a couple of water molecules.

Tony.

> <coot1.png><coot2.png>

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From: Tim Gruene 

Dear :),

electron density near special positions often bears some artefacts
because it is apparently difficult to calculate, i.e. the blob maybe
just some noise enhanced by its proximity near that two-fold axis.

Cheers,
Tim

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Dr Tim Gruene

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From: Artem Evdokimov

If you believe it to be rea density and not an artefact, this could be a wee PEG molecule, for instance...

Artem

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From: Jacob Keller


Who says this is on a twofold? Also, it would be very helpful to know
what was in the crystallization condition.

JPK

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Jacob Pearson Keller

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From: Greg Costakes

It would help if we knew the crystallization conditions and the protein solution components. Also, what are the map sigmas and e/A^3? It seems odd that there isnt positive density on the Fo-Fc map across the entire blob seen on the 2Fo-Fc map, considering you do not have anything modeled in. My guess is that your Fo-Fc map is at a much lower e/A^3 compared to your 2Fo-Fc map and what you are seeing is basically just greatly amplified noise. Try placing 3 waters in the blobs you see on the 2Fo-Fc map and see if that helps. 

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Greg Costakes