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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
