Maria, 1.7 A is too long for common diatomic molecules (N2, 1.1 A; O2, 1.2 A; CO, 1.1 A) or molecules like hydrogen peroxide (~1.48 A), methanol (ditto), etc.
Does the "water" have unusually low temp. factors (i.e., it's really a much heavier atom, and the peak you see is a Fourier ripple)? It may be indeed that you have (one) water at two alternate positions, but I think you need to reset to nothing modeled to be certain of density interpretaion moving forward. Thus, try removing the water you have already built, any surrounding waters or other ligands, and also the protein atoms to which all these are hydrogen bonded (set occ = 0), refine a few cycles, and then look at the diff. maps. Dave David Borhani, Ph.D. D. E. Shaw Research, LLC 120 West Forty-Fifth Street, 39th Floor New York, NY 10036 [EMAIL PROTECTED] 212-478-0698 http://www.deshawresearch.com > -----Original Message----- > From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On > Behalf Of Maria Håkansson > Sent: Friday, September 19, 2008 8:00 AM > To: [email protected] > Subject: Re: [ccp4bb] Unexplained electron density > > 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] > > >
