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If the atom in question is indeed a heavier atom, then I would expect
positive difference density. At Jacob's resolution (1.5A), I would
think there should be no problem in identifying what the molecule is
(at least, it should be possible to distinguish between MPD and
pyrophosphate or other classes of molecules, provided the occupancy
is reasonably high and there is no disorder. One more idea is to
process the data with anomalous contributions preserved, in which
case, any sulfur or phosphorous is likely to show up in anomalous
difference density maps.
On Apr 20, 2006, at 1:10 PM, Rizkallah, PJ ((Pierre)) wrote:
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Another suggestion: The atom with a low B-factor might be the S of
the
sulphonate group in HEPES or MES, as in buffers. Good Luck.
Pierre
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**
*******
Pierre Rizkallah, Daresbury Laboratory, Warrington, Cheshire WA4 4AD,
U.K.
Phone: (+)44 1925 603808 Fax: (+)44 1925 603124
e-mail: [EMAIL PROTECTED] html: http://www.srs.ac.uk/px/pjr/
-----Original Message-----
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On
Behalf Of
Jacob Corn
Sent: 20 April 2006 17:40
To: Segura Pena, Dario
Cc: [email protected]
Subject: Re: [ccp4bb]: Very low B factor after Refmac
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Hi Dario,
I would suspect that the MPD is not actually MPD, but instead
something
with a
similar makeup/geometry that contains an electron-dense atom, such as
phosphate.
For example, MPD looks like this
C C
\ /
C*-C-C (C2 marked by C*)
/ \ \
C O O
and pyrophosphate looks like this
O O O
\ \ /
P*-o-P
/ \ \
O O O
Not that I'm saying you have pyrophosphate in there (at 1.5A, you'd
probably be
able to see that extra oxygen). But you should consider all of the
other
things
enzyme may have either grabbed out of the drop or brought along
from the
cell.
Jacob
Segura Pena, Dario wrote:
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Dear all,
Recently I obtained protein crystal that grew in 60 % MPD. The
crystal
diffracts very well to 1.5 Ǻ. It seems that an MPD molecule
is in
the
active center of the enzyme, however the atom C2 of the MPD molecule
has a
B factor of 2 after several cycles of refinement with Refmac.
Does anybody have any idea why the there is such a low B factor for
this
atom?.The electron density for the region corresponding to the
atom C2
of
the MPD molecule is visible at 5 sigma level in a 2fo-fc map while at
3
sigma level there is not electron density for the rest of the
molecule.
I will appreciate any ideas or suggestions.
Sincerely,
Dario
--
Jacob Corn
The Berger Lab
UC Berkeley - Molecular and Cell Biology
[EMAIL PROTECTED]
phone: 510-643-8893
fax: 510-643-9290
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