I've had good luck using Phaser on test cases like that, but haven't
had access to a case that was previously unsolved. But in principle
it should work, if the model is good enough.
It sounds like you've thought about the resolution already, so this is
probably redundant. Anyway, the default of 2.5A is good for normal
sized molecules, but for very small molecules there might not be
enough observations, so you would want to change the default. If 2.5A
data would be suitable for a protein of 200 residues, then 1.5A would
give about the same number of reflections for a molecule of 40
residues. (Another way to look at this is that it will give about the
same ratio between the diameter of the molecule and the resolution
limit.) So I'd try 1.5A first, and if that didn't work I'd probably
try 1.1 and even 2.0 for completeness.
Another thing is that a peptide may not be as well conserved in
structure as you'd expect from the sequence, compared to a medium-
sized protein. So you might want to increase the RMS error deduced
from the sequence identity. (Of course, the data at a resolution
higher than a bit more than 2 times the estimated RMS error hardly
contribute to the likelihood function, so this may counteract the use
of higher resolution data to some extent.)
If the peptide is really flexible so that the model doesn't fit, then
that might explain why you can't solve the structure. As well,
structures with low solvent tend to be a bit harder.
Is your peptide reasonably spherical in shape, or is it asymmetric?
The current default in Phaser probably doesn't sample the angles for
highly asymmetric molecules finely enough to avoid rotating them too
much perpendicular to their long direction, so you might want to
increase the sampling in the rotation search.
As you imply, if a crystal diffracts to 1.1A, then you'll probably
have a decent anomalous signal from the intrinsic sulfur atoms. Once
you've got a license for SHELXD, HySS or SnB, you can probably
complete the structure in a variety of ways -- with atomic resolution
data, you can even ask Phaser (now using the SAD target instead of the
molecular replacement modes) to complete with S and C atoms, and it
will probably build a complete model.
Best wishes,
Randy Read
On 19 Jun 2009, at 17:26, Sickmier, Allen wrote:
I am trying to do molecular replacement on a small peptide (less
than 40 AA) and have not had any success using phaser. Are there any
tricks or better programs for really small peptides?
The data is great 1.1 A, ~35% solvent, and two molecules in the ASU.
I have tried all the standard stuff, changing resolution cut off
etc. I may move to sulfur phasing at this resolution but I would
like to get the MR to work.
Allen
------
Randy J. Read
Department of Haematology, University of Cambridge
Cambridge Institute for Medical Research Tel: + 44 1223 336500
Wellcome Trust/MRC Building Fax: + 44 1223 336827
Hills Road E-mail: [email protected]
Cambridge CB2 0XY, U.K. www-
structmed.cimr.cam.ac.uk
