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 100% sequence id (i.e. the same protein) is not enough
for MR, if the protein has undergone a big conformational change -
sometimes 20-25% sequence identity may be enough.
Does you model have more than one domain? In that case it may be
useful looking for the domains separately or prepare search models
with different, likely, orientations of the domains.
Another thing: Phaser with default parameters throws away solutions if
the proteins overlap after crystallographic symmetry, even only a
little bit. You may want to remove loops/ends from your model which
you think may be flexible, and/or change the default parameters of
Phaser to allow more Calphas to overlap.
Mark
Mark J. van Raaij
Dpto de Bioquímica, Facultad de Farmacia
Universidad de Santiago
15782 Santiago de Compostela
Spain
On 22 Jun 2009, at 04:15, 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 models have been searched according self-rotation criterion.I
> build the model using Phenix and Arp/wArp,but there are no good
> results.The best result is R/Rfree 0.47/0.48.Also,I do MR with Phaser
> and Molrep.The Phaser indicate Z-scores 6.5 and no good
> results,neither do the Molrep.I am very confused about several
> questions:
> 1.Just 30% identity model can be used for MR model?What at
> least identity should be acquired for MR?
> 2.Are there good program editing the model except Chainsaw?
> 3.How can I make sure my rotated and translated MR model is
> right and can be used for next model building and refinement?
>
>
> --
> Best
> Wishes!
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