Unidentified density

From: Sudhir Kumar
Date: 10 February 2012 06:06

Dear all,
 I have a 2 A structure of an enzyme which show 12 molecules per asymmetric unit. While placing waters i found out some blobs where i could not model any ligand. It is surrounded by 3 Asp molecules. I have attached screenshot of the blob at 1.5 sigma cutoff 2fo-fc density. Crystallization condition had following precipitants: PEG 1000, Peg 3350, MPD, Ethylene glycol,and protein contained Glycerol.  My protein is known to bind Cysteine/Serine, though i haven't added any in crystallization buffer. any suggestion what it might be are welcome. thanks in advance

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best regards
Sudhir Kumar

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From: Vandana Kukshal


hi sudhir, 

  i think in second snapshot you can fit MPD as its structure is seems similar. ..... 

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Vandana kukshal

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From: <Herman.Schreuder

Dear Sudhir,

 

A blob surrounded by three Asp residues looks like a positively charged ion. What else (buffer, additives) is in your crystallization drop? I would also try to fit cysteine/serine. At 2 Å you will quickly see whether or not this is correct.

 

Good luck!

Herman