*** For details on how to be removed from this list visit the ***
*** CCP4 home page http://www.ccp4.ac.uk ***
I would be very suspicious of "general rules" derived from an
analysis of low-resolution structures found in the PDB. If that
analysis says "people don't place waters into their structures at
3.5Å", then that does not necessarily mean that it is never justified
to place waters at 3.5Å. As Martyn rightfully pointed out, that
analysis may say more about "people", i.e. model building and
refinement practices, than about objective physical reality (whatever
that is).
I think the issue really is that somebody is observing a feature in
the electron density at 3.5Å and attempts to explain that feature. To
treat that situation in a rather formal way, the first step would be
to create a list of (plausible) hypotheses for an explanation. Let's
assume that a water molecule could satisfactorily explain that
density feature. When is it "allowed" to include the water molecule
in the model, and when not? Clearly, crystallography on its own,
particularly at a resolution of 3.5Å, is not really suitable to
_prove_ that a feature is a water molecule and not an ion or an FFT
ripple or noise, or something else. Additional information is needed
to increase the confidence that the feature is indeed a water
molecule. For example, if there are similar high-resolution
structures that "show" a water molecule, then I think it is perfectly
legitimate to include that water molecule in the model for the 3.5Å
structure. After all, that is how many features are interpreted at
that resolution. Many times, people brush features aside, saying
that's just "noise". What is the objective justification for that?
Model building and refinement make use of a lot of external
information about structural properties of amino acids, nucleic
acids, etc., even at very high resolution and even more so at low
resolution. I think we can just as well derive some "general" rules
from _high_resolution structures about waters and use those rules to
interpret low-resolution structures, just like Jack alluded to in an
earlier post.
That does not mean one should now drown all low-resolution structures
with waters. It only means that things are never really simply black
and white. They often are green and blue and red...
On Mar 31, 2006, at 9:24 AM, Bart Hazes wrote:
*** 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
======================================================================
========
------------------------------------------------------------------------
--------
Mischa Machius, PhD
Associate Professor
UT Southwestern Medical Center at Dallas
5323 Harry Hines Blvd.; ND10.214A
Dallas, TX 75390-8816; U.S.A.
Tel: +1 214 645 6381
Fax: +1 214 645 6353
