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 <[EMAIL PROTECTED]>:
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 [EMAIL PROTECTED]
--
============================
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 [EMAIL PROTECTED]
