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Subject: Re: unknown density
From: Roger Rowlett rrowlett {- at -} COLGATE {- dot -} EDU
Date: 2010-02-03
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I agree with many others: this is quite possibly sulfate or phosphate.
If collected at 1.54A the anomalous map should help identify the
presence of sulfur. Sulfate or phosphate may be present at lower than
full occupancy. I would refine everything else you reasonably know in
the model (including water and any other anions, ligands, etc.) and see
if the blob of density sharpens up. Usually a sulfate looks like a
sphere of density, and a sulfate + water may be somewhat elongated. If
the difference map without modeled anion looks reasonable, try a
sulfate of phosphate at 1.0 or 0.5 occupancy to see if the 2Fo-Fc and
Fo-Fc maps still look reasonable. There is plenty of precedent for
sulfate/phosphate binding near Glu and Arg residues. If you have
negative Fo-Fc density when using sulfate at 0.5 occupancy, you may
have no other reasonable choice than to model with water (or nothing at
all), with the acknowledgment that this may not be completely correct,
either.
Cheers.
On 2/3/2010 12:17 PM, Katja Schleider wrote:
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style="font-family: inherit; font-style: inherit; font-variant: inherit; font-weight: inherit; font-size: inherit; line-height: inherit; font-size-adjust: inherit; font-stretch: inherit; -x-system-font: none;"
valign="top">Dear all,
I found some fairly substantial density in the active site of my
protein structure. But I don´t know what it should be. My
crystallisation condition consists of lithium sulfate,
citrate-phosphate and peg1000. The whole lot doesn't make a dashed bit
of sense! Any suggestions to fill this density with something?
Picture is attached.
Thanks a lot,
Katja
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