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On a related issue, we found that highly conserved water molecules tend to be present in both cryo structures and room temperature ones. > From: Bart Hazes <[EMAIL PROTECTED]> > Reply-To: <[EMAIL PROTECTED]> > Date: Fri, 31 Mar 2006 08:24:40 -0700 > To: Martyn Winn <[EMAIL PROTECTED]> > Cc: Prem kumar <[EMAIL PROTECTED]>, ccp4bb <[email protected]> > Subject: Re: [ccp4bb]: solvent at low resolution > > *** For details on how to be removed from this list visit the *** > *** CCP4 home page http://www.ccp4.ac.uk *** > > > > A lot of the structures analysed by Carugo and Bordo were done at room > temperature. We and others found that you see about double the number of > waters in cryo-structures and at least in the 1.8 to 0.8 Angstrom range > we didn't see the number increase much, at least not for first shell > waters. I don't know how this holds up at moderate resolution, but at > low resolution it remains in my opinion hard to convincingly prove there > is a water. After all if Carugo and Bordo predict zero waters at 3.5 A > and more recent data suggests there are twice as many at 100K then that > still amounts to zero waters. > > Bart > > PS: other effects of cryo cooling can be found in > Dunlop et al. (2005) Pros and cons of cryocrystallography: should we > also collect a room-temperature data set? Acta Cryst D61, 80-87. > > Martyn Winn wrote: >> *** For details on how to be removed from this list visit the *** >> *** CCP4 home page http://www.ccp4.ac.uk *** >> >> >> >> The analysis of Carugo and Bordo, Acta Cryst D55, 479 (1999) >> as implemented in the CCP4 program RWCONTENTS, suggests >> that you shouldn't see any waters at 3.5A. >> >> Their analysis was based on PDB structures, so this just >> confirms your own observations. And it is therefore based >> on working practice rather than any explicit justification. >> >> Of course, this is only a guide, and doesn't preclude >> identifying e.g. well-defined conserved water sites. >> >> Cheers >> Martyn >> >> On Thu, 30 Mar 2006, Prem kumar wrote: >> >> >>> *** For details on how to be removed from this list visit the *** >>> *** CCP4 home page http://www.ccp4.ac.uk *** >>> >>> >>> Dear all, >>> >>> I am refining structure at 3.5 A resolution. the >>> protein has 340 residues. CNS water_pick gave me 80 >>> water molecules. out of that ~50 are in resonably good >>> density. when i go through PDBs at this resolution >>> many people didnt add water. my question is, can I add >>> water molecules in this resolution, or upto what >>> resolution. please quote if any reference regarding >>> this case. >>> >>> Thanks in advance! >>> >>> with regards >>> prem >>> >>> >>> >>> ====================================================== >>> R. Prem kumar >>> Research Scholar, >>> Department of Biophysics, >>> All India Insitute of Medical Sciences(AIIMS), >>> New Delhi-110029. >>> INDIA >>> Phone: +91-11-26593201, 9810304855 >>> ====================================================== >>> >>> __________________________________________________ >>> Do You Yahoo!? >>> Tired of spam? Yahoo! Mail has the best spam protection around >>> http://mail.yahoo.com >>> >> >> >> >> >> ************************************************************************** >> * * >> * Dr. Martyn Winn * >> * * >> * Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, ENGLAND * >> * Tel: +44 1925 603455 E-mail: [EMAIL PROTECTED] (personal) * >> * Fax: +44 1925 603825 E-mail: [EMAIL PROTECTED] (CCP4 problems) * >> * URL: http://www.ccp4.ac.uk/martyn/martyn.html * >> ************************************************************************** >> >> > > > -- > > ============================================================================== > > Bart Hazes (Assistant Professor) > Dept. of Medical Microbiology & Immunology > University of Alberta > 1-15 Medical Sciences Building > Edmonton, Alberta > Canada, T6G 2H7 > phone: 1-780-492-0042 > fax: 1-780-492-7521 > > ==============================================================================
