Hi All,
The situation is complicated, and I am a first yesr PHD student.
The data is not good (3A). Another protein in the same family has been
published recently, so that we could use Molecular Replacement.
Matthews's Coefficient suggested that there are two molecules in
the asymmetric unit, however, we could only find one. It fits pretty well.
And, we have a set of SeMet data. The two Se peaks are exactly on the
sulfuers of the two Mets (that's very convincing, right?) Phaser and CNS
gave us similar solutions. Anyway, then I started to build, and I found a
problem: there's one DNA base pair missing in the complex (The DNA we used
is longer than the model, so I needed to add back a few DNA base pairs. I
need to add back two base pairs at each end, so between two symmates I
expect electron density for four base pairs, right? But I only got density
for three. I really couldn't understand.The only explaination I can come up
with is that the DNA used in crystallography was wrong, but maybe someone
could give me a few other possibilities.)
We checked the space group again. Rmerge of P31 didn't seem better
than P3121. The problem of missing density for DNA still exists...
Maybe I haven't described my problem clearly... sorry for
bottering... Any suggestion and comment are welcome. Thanks!
Xun Lu
Department of Molecular and Structral Biochemistry
North Carolina State University
