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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:
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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:
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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
======================================================
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