molecular replacement...

Zbyszek Otwinowski zbyszek at
Thu Apr 17 11:33:16 EST 1997

sai at wrote:
>            i'm planning to crsytallize and solve the structure of the
> protein that i'm working on.  there are no homologous structures that
> hve been reported for my protein.  but i would like to take advantage of
> the fact that i have a thioredoxin fusion protein and the structure of
> the thioredoxin protein has been determined.  my protein is 52.5 kDa and
> the thioredoxin is ~11.6 kDa, making the total mass of my fusion protein
> at around 64.1 kDa.  I would like to know how much homology i need to be
> able to reliably use the solved structure of the thioredoxin (comprising
> abour 18% of the fusion protein) as molecular replacement to solve the
> structure of my protein???

Molecular replacement, in practise, needs to account for at least 50% of
the total structure. The 50% limit is not a hard limit, maybe 40% in
cases can be enough. One has to account also for the search structure
not being identical to its equivalent in the crystal, in such cases only
some fraction of search structure is being used in molecular replacement

> i want to know this in hopes of avoiding
> doing heavy atom derivatives (or is that just too inevitable)

doing heavy atom derivatives (or MAD) is inevitable

  Zbyszek Otwinowski                     |        zbyszek at
  University of Texas                    |        tel : (214)-648-5098 
  Southwestern Medical Center            |        fax : (214)-648-5095 
  5323 Harry Hines Boulevard  Dallas, Texas  75235-9038

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