Fred,
Two cents - I think the P1 SAXS solution should strongly guide your choice
of symmetry constraint above all else in this case: do any of the
symmetry-restrained shape reconstructions *improve* the statistics (chi) and
stability of the shape (NSD) when compared to the P1 result? Also, it sounds
like you have other data - do the theoretical Rs, f/fo, etc of the shapes
generated agree well with your other measurements?
Cheers,
Kushol
Kushol Gupta, Ph.D.
Research Associate
Van Duyne Laboratory - HHMI/Univ. of Pennsylvania School of Medicine
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215-573-7260 / 267-259-0082
Of course, 222 has not a 4 axis, otherwise it would be a 4-fold axis.
But that's the output of the program. P4 exp. model has a 4-fold axis
along the longest axis, while the P222 MODEL has a 4-fold axis along the
smallest, which doesn't make any sense. Can you imagine something build
up with 4 identical subunits and 222 symmtry, but without a 4-fold axis
at the molecular level (I mean at the envelop resolution level)?
Em 29-07-2010 12:32, Vellieux Frederic escreveu:
> Hi,
>
> To quote you: "even my P222 experimental envelop does have a 4-fold
> axis" - this is not suprising, a particle with 222 symmetry does not
> have 4-fold symmetry. There are 3 mutually perpendicular 2-fold axes
> that intersect at the origin (of the "particle", of the molecule) [and
> for the nomenclature, these axes are named the P Q and R axes].
>
> Fred.
>
> Fred wrote:
>> Thanks all of you who promptly replied my question.
>> I should have been more precise. I was referring to the symmetry of
>> the tetrameric particle (point symmetry) at the molecular level not
>> at the atomic level. This question has arisen because I have
>> collected some SAXS data of my protein in solution and I don't have a
>> molecular model to superpose to the experimental envelop. Others
>> experimental data, gel filtration and NAT-PAGE, suggest a tetrameric
>> particle. On the other side, P1, P2, P222 and P4 experimental
>> envelops are quite different. So, I am not sure which symmetry to
>> take. Considering the native state (no ligands at all), 4 identical
>> subunits and that the interface of oligomarization have to be
>> conserved, I would take P222 or P4. However, I can be able to imagine
>> such spacial arrangement without a 4-fold axis at the molecular
>> level. Indeed, even my P222 experimental envelop does have a 4-fold
>> axis.
>> I appreciate if you could add some more comments on this.
>> Thanks in advance,
>> Fred
>
>
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