I think I would be tempted to chainsaw one of the ensemble chains of
2IT8 (they look very similar except for side-chain disposition) and use
1 or 2 of these as search models in a Phaser run. If this works, you
should see good Z-values and the final result inspected in Coot should
show good molecular packing with clear solvent channels and no isolated
molecules. Electron density should look reasonable, and if there are any
known non-protein features (like metal ions) they should clearly show up
in difference density.
If the initial Phaser solution looks OK in terms of packing, I would be
tempted to take the phased generated and, using the sequence of your
protein, subject it to auto-building with Parrot and Buccanner, using
2-fold NCS (if you do in fact have 2 molecules in the ASU). With any
luck, you should be able to auto-build 90% of your model. This approach
worked for us for a medium resolution problem with 8-fold symmetry for a
really marginal search model.
_______________________________________
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: [email protected]
On 6/29/2015 3:10 PM, xaravich ivan wrote:
Hi everyone,
I think I have finally got a solution in Phaser (screen shot attached)
as the TFZ is 10.
However the solution PDB has 30 molecules in it as the search model
was an NMR solution.
As I have 0.944 Angs resolution data pretty complete, I thought of
building the initial model in ArpWarp.
I prepared a new PDB file form the Phaser solution output with only
one molecule instead of 30. Prepared the sequence file in pir format
for the target. Now the wilson plot says B-factor of 3.66 and solvent
content 0.98 even if I cut off the low resolution data to 8.0 from
20.0 and increase the high resolution to 1.0.
Initially when I calculated the mathews coefficient it showed the best
estimate to be 2 molecules in the assymmetric unit.
Am I missing something again?
Thanks in advance,
Ivan
