Hi Nishant
AMPLE can work with ensembles from NMR structures
(http://ample.readthedocs.io/en/latest/examples/rst/nmr_ensemble.html#example-nmr-ensemble;
see https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3817692/) or sets of
distant homologues
(http://ample.readthedocs.io/en/latest/examples/rst/homologs.html#example-dist-homologs),
trialling a large number of edited variant ensembles (from mildly
truncated to brutally) in an automated fashion. With AMPLE you select
Phaser and/or Molrep for the actual MR step and, resolution permitting,
can use Shelxe's statistics to give you a particularly clear indication
of success/failure.
Good luck
Dan
On 29/08/17 13:31, Randy Read wrote:
Hi,
Molecular replacement gets progressively more difficult as the
sequence identity drops, though the correlation between sequence
identity and model quality is not perfect. With the best models
having sequence identities around 24%, success is by no means
guaranteed, so you might have to try lots of strategies or resort to
experimental phasing. NMR models do tend to be worse for molecular
replacement, so that will probably lower the chances of success further.
In addition to what others have said already, it's worth mentioning
that, in a number of very difficult structure determinations (best
models around 20% sequence identity), the key thing that made the
difference between failure and success was pruning off the parts of
the ensemble that do not agree among the members of the ensemble,
leaving just the conserved core. This can be done, for instance, in
the Ensembler program with the "trim=True" flag. For this to work
best, it's helpful if you happen to have a number of potential models
that are also relatively distantly related to each other, to really
highlight what is conserved in the fold.
Best wishes,
Randy Read
On 29 Aug 2017, at 12:42, Andreas Forster <[email protected]
<mailto:[email protected]>> wrote:
Dear Nishant,
Rosetta is a good suggestion. You can also use an ensemble of
several related (superposed) structures as your search model. This
will improve your chances of success.
All best.
Andreas
On Tue, Aug 29, 2017 at 12:50 PM, Nishant Varshney <[email protected]
<mailto:[email protected]>> wrote:
Dear Crystallographers,
I am working to solve an human protein structure which has a
domain sequence identity of 24% with domain of another protein.
As Phaser as well as Molrep failed to give any definite solution
(TFZ=3.7 from MR), I want to ask, if solution structure of
another protein having domain sequence similarity of 25% or a
homology model can be used as a template for MR?
Many thanks and Regards
Nishant
--
Dr. Nishant Kumar Varshney,
Research Associate,
C/O Dr. Sameena Khan,
Drug Discovery Research Center,
Translational Health Science and Technology Institute (THSTI)
NCR Biotech Science Cluster,
3rd Milestone, Faridabad – Gurgaon Expressway,
Faridabad – 121001 (HARYANA), India
Ph: +91- 0129-2876477 <tel:+91%20129%20287%206477>
Mob: 8390564690
------
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] <mailto:[email protected]>
Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk
<http://www-structmed.cimr.cam.ac.uk>
--
Dr Daniel John Rigden Tel:(+44) 151 795 4467
Institute of Integrative Biology FAX:(+44) 151 795 4406
Room 101, Biosciences Building
University of Liverpool http://pcwww.liverpool.ac.uk/~drigden/
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