Dear Haytham,
I do not think your unknown density is DTT. As far as I can judge from
the pictures you sent it looks like an Asp or a Glu binding to a large
spherical density which may be a metal ion (tin?). You can calculate an
anomalous map in ccp4i with the program FFT, using model phases and
selecting "anomalous" as map type.
In your case I would go over all components present in the
crystallization solution, look for some heavy atom to fit in the
spherical density and try to fit an Asp or a Glu in the density where
you tried to fit the DTT. Especially when working with proteases, small
peptide fragments or even single amino acids may be present due to the
action of the protease. If you are working with another type of protein,
a small peptide fragment or amino acid may be carried along during the
purification process. Of course, if your crystallization solution
contains other molecules which might fit the density, you should try
those as well.
Good luck!
Herman
________________________________
From: CCP4 bulletin board [mailto:[email protected]] On
Behalf Of Haytham Wahba
Sent: Friday, June 03, 2011 8:51 PM
To: [email protected]
Subject: [ccp4bb] anomalous difference map?
preliminary question??
resolution 1.5
crystal soaked in dimethylTindibromide + DTT
dimer in Asymmetric U.
one show diMethylmonobromidetin only no DTT (not shown)
other subunit show (almost) monomethylmonobromideTin + DTT (see
attached)
even after refining individual atom (phenix) i still have positive and
negative peak
and no density of DTT for sulfhdryl group away from tin (see attached
sim-Ann-diff)
including 2 DTT molecules (diasteriomers) the situation getting worse
(see attached)
good r-factors good Molprop
1- helpful comment will be appreciated
2- i want to calculate anomalous difference map for Br , sulfur and Tin
(not refining using anomalous) how can i do that?
thank you in advance
haytham wahb
canada
UdeM
Biochemi
