A few thoughts:
1. Search for all possible space groups (e.g., P2 and P21 in this
case). Be happy it isn't C222, which means 8 possible combinations
of screw axes to search! As mentioned already, P21 is far more
common than P2. I think P21 is one of the most common space groups
in protein crystallography.
2. How are you determining how many copies of the search model go in
the ASU? It is not necessarily one biological unit, or an integral
number of biological units. Run a cell content analysis in Phaser
(e.g. Matthews probability calculator) and start there, but consider
the results a suggestion only. For larger ASUs, the predicted number
is not very accurate. "Six" might actually be 4 or 8 chains.
3. Look at the crystal packing in Pymol, Coot, or in you favorite tool.
You can do this by enabling a large symmetry molecule radius. If you
see a regular lattice of proteins with nice solvent channels and
protein-protein contacts, things are looking up. (But you can be
fooled into a premature victory at times.)
4. Partial Phaser solutions may provide a big hint about how many
molecules are in the ASU when packing is examined. Often the
placement of the missing molecules is quite obvious, as it completes
a solvent channel or fills in symmetrical protein-protein contacts.
5. Finally, look at the maps. Crappy maps probably mean the wrong space
group, especially if chains don't pack well. Good maps with good
packing usually mean you are on the right track.
Cheers and good luck,
_______________________________________
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 8/1/2012 2:27 PM, Uma Ratu wrote:
Dear All:
I try to use Phaser to solve the structure by Molecular Replacement.
The data set is collected @180 degree. I process the data using HKL,
and have resonable good score: rejection (0.05), Linear R-factor
(0.038), completeness (98.3), resolution (50-1.5).
I then use Phaser to do MR. The parameter setting are:
automated search
components in asymmetric unit; number of residue 1332; number in
asymmetric unit 1
perform search search using "ensemble1" number of copies to search for 4
The protein is in tetramer form. I define this by using the residue
number (1332) which is 4 x monomer.
After run, Phaser only gave 9 partial solutions, and no solution with
all components. The resulted PDB contains only dimer form of the
protein, not the tetramer. And the first TFZ score is around 2.5,
which is too low for MR.
I have the report file of data processing and the summary of Phaser
attached.
Could you please advice which part is wrong, why can I get the
tetramer form of the protein?
Thank you
Uma
