For large copy number MR solutions, we have found that EPMR is a good
alternative to Phaser when the latter doesn't find a solution. However,
we also have noted in some experimental testing that both Phaser and
EPMR have some difficulties with copy numbers greater than 4-6. Another
alternative, if you have lots of patience, is Queen of Spades. It can
sometimes place large numbers of models in the ASU at the cost of a
loooooooooong wait. But a CS collaborator and I found that genetic
algorithms (e.g. EPMR) were pretty efficient at large copy number searches.
If you can place a handful of protein chains in the ASU, you might be
able to get away with searching with some dimer or tetramer units from
that partial solution. That's what I wound up doing with a
6-chains-per-ASU problem a few years ago (PDB 2A8D). The 3-dimer search
in EPMR worked like a charm, whereas the 6-monomer search was hopeless
at the time.
Cheers,
_______________________________________
Roger S. Rowlett
Gordon & Dorothy Kline Professor
Department of Chemistry
Colgate University
13 Oak Drive
Hamilton, NY 13346
tel: (315)-228-7245
ofc: (315)-228-7395
fax: (315)-228-7935
email: rrowl...@colgate.edu
On 4/30/2012 11:41 AM, Ke, Jiyuan wrote:
Dear All,
I have a question regarding solving a crystal structure by molecular
replacement. It is a single protein with a molecular weight of 25.5
kDa. The cell dimension is rather big from the diffraction data ( 90.9
Å, 143.9 Å, 216.3Å, 90°, 90°, 90°). The possible space group is
P212121. With such a big unit cell, we predicted that there are 8-10
molecules per asymmetric unit. We have a decent model with sequence
similarity of 49%. I tried several times with Phaser search with the
current model and had difficulty to find any clear solution. Has
anyone seen such cases and any suggestions to solve the structure? Thanks!
Jiyuan Ke, Ph.D.
Research Scientist
Van Andel Research Institute
333 Bostwick Ave NE
Grand Rapids, MI 49503
