RE: [Q] Experimental phases only structures

["Ditlev Brodersen" <ding@imsb.au.dk>]

***  For details on how to be removed from this list visit the  ***
***    CCP4 home page http://www.dl.ac.uk/CCP/CCP4/main.html    ***

Hi Tzanko,

> I am preparing a structure for a publication and came to a standstill
> about references involving structure determination based on experimental
> phases only (no protein atoms contribution). The only reference I found
> is Burling et al, 1996.
>
> 1. Would you please let me know if somebody else has published a
> structure determined that way?

Basically, all structure determinations that do not involve molecular
replacement (MIR/SIR/MAD etc.) are based on experimental phases! What Burling
and Brunger did in 1996 was not to solve the structure of rat MBP (it was solved
by Hendrickson by MAD in 1991), rather to produce an improved set of
experimental phases by using the powerful anomalous signal available from the
bound Yb3+. The only way that this experiment differs from what we all do is
that their phases were so good that they need not perform any kind of density
modification and thus could look at a map virtually free of bias from model
atoms at 1.8A.

> 2. What do you think about such an approach? Why aren't there more
> crystal structure determinations like Burling et al., 1996?

Obviously, good experimental phases to 1.8A is what everybody wants, the problem
is that most isomorphous derivatives whether they're used for MIR(AS) or MAD
usually give worse phases because of various malicious combinations of
nonisomorphism, high B-factor etc. What makes Burling's approach so powerful is
that they've substituted a naturally bound calcium ion for the lanthanide. The
heavy atom is thus bound much tighter than a loosely associated, soaked heavy
atom would be.

For your interest, we did something similar for one of the EF-hand proteins:

Brodersen, D.E., Etzerodt, M., Madsen, P., Celis, J.E., Thøgersen, H.C., Nyborg,
J., and Kjeldgaard, M. (1998) "EF-Hands at Atomic Resolution: The Structure of
Human Psoriasin (S100A7) Solved by MAD Phasing", Structure, 6: 477-489

  -- Ditlev

-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-
      __
     /_/\       Ditlev E. Brodersen       Phone: +45 8942 5021
    / /\ \      M.Sc., Ph.D. student      Fax  : +45 8620 1222
   / / /\ \     IMSB, Aarhus University   Email: ding@imsb.au.dk
  / / /\ \ \    Gustav Wieds Vej 10c      WWW  : http://imsb.au.dk/~ding/
 / /_/__\ \ \   DK-8000 Aarhus C
/_/______\_\/\  Denmark
\_\_________\/