Hello David and others,
Thanks for yur comments.
I guess it might be as simple as water molecules, present in the
structure but not at the same time.
The density looks like a rod with uneven distribution. Both ends of
the rods (1.7-1.8 Å in between)
make hydrogen bonds to protein or other water molecules - normal
distances (2.3-3.3 Å). Could it be
strong water molecules but with partial occupancy meaning that both
sites are occupied but not at the same time?
I guess refmac automatically refines the molecules that way although I
have not specified it in my file. So after
refinement as too close water molecules there is no clash just nice
density. However I assume it is appropriate to
specify these water molecules as the same water but with an
alternative conformation in the pdb file.
Best Regards,
Maria
19 Sep 2008 kl. 11:10 skrev David Briggs:
> Hi Maria,
>
> Initial questions:
> 1) What's present in crystallisation/purification buffers?
> 2) Are any other ligand visible for the 9sigma peak?
> 3) Does the 9 sigma peak also have a peak in an anomalous difference
> map?
>
> Assuming 1.7A is accurate (and with 1.5A resolution, you'd hope it
> would be!) a metal-ion - water interaction is looking less likely.
> Take a look at Marjorie Harding's papers and website for target metal
> ion - ligand distances, and the closest you'll see is water:Mg2+, at
> 2.07.
>
> http://tanna.bch.ed.ac.uk/newtargs_06.html
>
> So one would assume it is a covalently bonded compound.
> So back to question 1.
>
> What's in your buffers?
> A quick search for bond length tables suggests Carbon-Sulphur (1.8)
> and Carbon-Chlorine at 1.7.
>
> hope this helps
>
> David
>
> 2008/9/19 Maria Håkansson <[log in to unmask]>:
>> Hello All,
>>
>> I have a problem with a 9 sigma positive peak 1.7 Å away from a water
>> molecule (or what I believe is
>> a water molecule). There are several similar peaks in my map though
>> only one
>> is as high as 9 sigma.
>>
>> My first thought was to exclude these too close waters. However the
>> R-values
>> increased by more than 0.5 %. Could it
>> be carbonmonoxide or oxygen atoms? By the way, It is 1.5 Å
>> resolution data.
>> Any suggestions?
>>
>> Best Regards,
>>
>> Maria Håkansson
>>
>>
>>> Maria Håkansson, Ph.D.
>>> tel: +46 (0) 76 8585 706
>>> Senior Scientist, Max-lab, Lund University
>>> fax: +46 46 222 47 10
>>> Ole Römers väg 1 (P.O. Box 188)
>>> www.maxlab.lu.se
>>> SE-221 00 Lund, Sweden [log in to unmask]
>>>
>>
>
>
>
> --
> ============================
> David C. Briggs PhD
> Father & Crystallographer
> http://drdavidcbriggs.googlepages.com/home
> AIM ID: dbassophile
> ============================
> Maria Håkansson, Ph.D.
> tel: +46 (0) 76 8585 706
> Senior Scientist, SARomics Biostructures AB fax: +46 46 19 12 77
> Scheelevägen 22 (P.O. Box 724) www.saromicsbiostructures.com
> SE-220 07 Lund, Sweden [log in to unmask]
>
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