DEAR ALL
I am trying to solve the structure of a protein DNA complex with molecular
replacement. The resolution in about 2.5 angstrom. The spacegroup is P21.
The search model has about 50% identity and is a dimer of a dimer. The
problem is the unit cell is huge and so the number of molecules in
Try using DNA as a search model - this has worked very successfully in our
hands before.
Tony.
- - - - - - - - - - - - - - - - - -
Dr Antony W Oliver
Senior Research Fellow
CR-UK DNA Repair Enzymes Group
Genome Damage and Stability Centre
Science Park Road
University of Sussex
Falmer, Brighton,
In addition to that good suggestion, with a model at such high sequence
identity and with reasonable resolution data, it would be a good idea to search
for smaller models, like a single dimer or even a monomer, because the assembly
may have changed conformation. Another possibility you should
]
Envoyé : jeudi 24 juillet 2014 13:50
À : CCP4BB@JISCMAIL.AC.UK
Objet : [ccp4bb] Problem in molecular replacement
DEAR ALL
I am trying to solve the structure of a protein DNA complex with
molecular replacement. The resolution in about 2.5 angstrom. The
spacegroup is P21. The search model has
@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK
Objet : [ccp4bb] Problem in molecular replacement
DEAR ALL
I am trying to solve the structure of a protein DNA complex with molecular
replacement. The resolution in about 2.5 angstrom. The spacegroup is P21.
The search model has about 50% identity
30% is getting difficult - it may or may not work. But it is worth
trying.
Search model preparation programs such as Chainsaw rely on an accurate
sequence alignment (between model and target), and this also gets
difficult at 30%. You should try something more sophisticated than
simple pairwise
Hey!
I have found the FFAS server ( http://ffas.ljcrf.edu/ffas-cgi/cgi/ffas.pl )
to build the best models for low homology MR searches. A relevant paper:
2004 Acta Cryst D60 1229-1236.
Best of luck,
Frank
2009/6/21 孙建 sunjian00...@gmail.com
Dear all:
Recently,I have a problem
孙建 wrote:
Dear all:
Recently,I have a problem about molecular replacement with
identity 30% model. There are two moleculars in AU.Through
self-rotation analyze,there are a two-fold axis in AU along X axis or
Z axis.Then I rotate and translate the model with CNS MR module.
several
Dear Sunjian,
what is important is the structural similarity of your model to the
unsolved structure, for instance in r.m.s.d - of course, this cannot
be determined until you have solved the structure!
The % identity is only an indication of how similar the structures may
be, sometimes
Dear all:
Recently,I have a problem about molecular replacement with
identity 30% model. There are two moleculars in AU.Through
self-rotation analyze,there are a two-fold axis in AU along X axis or
Z axis.Then I rotate and translate the model with CNS MR module.
several models have been
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