Ethan Merritt schrieb:
> Hi all,
>
> I have an interesting problem case at the moment.
> We have crystallized the same 2-domain protein in two different,
> i.e. non-isomorphous, crystal forms.
>
> There is a decent homologous structure for one domain
> (about 40% of the total), but no known homologous structure for
> the larger second domain. Phaser easily places the probe structure
> in both unit cells, but recovering the remaining 60% of the structure
> from that starting point is problematic.
>
> In both cells there is only a single copy of the protein per a.s.u.,
> Resolution is on the order of 2.6A, and the solvent content is
> relatively low. So no help from NCS or solvent flattening for
> either structure by itself.
>
> Yes, we can start searching for derivatives or SeMet data, but
> meanwhile I am looking for advice on the current generation of tools
> available for cross-crystal density averaging.
>
> Are there any that tie in to auto-tracing in Arp/wArp or resolve?
> Is there any chance of eventually doing joint refining of both structures
> simultaneously?
>
Ethan,
I would try to
a) chop the homologous structure into 2ndary structure elements and
rigid-body refine those,
b) adjust the sequence and fit the mutated side chains into their
density, using Coot
c) do some restrained refinement in refmac
check the R_free after a), b), c) and pick the best structure based on
that. Then run buccanneer - it has worked for me once in a similar case.
best,
Kay
--
Kay Diederichs http://strucbio.biologie.uni-konstanz.de
email: [log in to unmask] Tel +49 7531 88 4049 Fax 3183
Fachbereich Biologie, Universität Konstanz, Box M647, D-78457 Konstanz
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