Dear Ping,
First thing to ask: Do you know with 100% certainty if your crystals
contain a complex? If your crystals are large enough (and you have more
than one) you can check this on SDS-PAGE or with mass-spec as long as
you are sure to remove all surrounding mother liquid that may
contaminate your result. Both proteins should be observed very clearly
(80%-20% would be a contamination rather than a co-crystal!). Experience
tells us that even with high affinity (nanomolar or better) and
preformed complexes, still often only one of the two partners will
crystallize.
Second: does your second protein contain more than one domain? If so,
there may be domain movements that obscure the desnity or even lead to a
completely wrong MR solution. Try rigid body refinement with individual
domains first. If this does not work, try MR with the individual domains.
The MR solution of your second protein may also be wrong for any other
reason. Check if you can trust the solution based on the statistics
provided in the log file. If the LLG is only marginally better after
adding the second protein, it will probably be wrong. Check also if
there is no real solution hanging around but rejected by the program
because (for example) it has just one clash too many.
Remy Loris
Vrije Universiteit Brussel and VIB
On 04/12/11 05:18, Ping Wang wrote:
>
> Dear all,
>
> Recently I have a dataset with a protein complex including two
> proteins. Each structure of the single protein is available. When I
> use phaser to solve the phase, one protein got good density while the
> other was not so ideal. In order to get a better phase, I try to cut
> the flexible region of the bad protein. But the result shows no
> improvement. Does anyone have some suggestion for me? Thanks!
>
> Ping
>
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