I think the relevant point in this discussion is that the original paper
discussed the apo and substrate complexes of the protein. For the
structure with lower resolution data you may indeed get a better model
by taking the high resolution model and just applying rigid body
refinement to it. After that step you would like to find and model the
differences between the two structures. This includes the bound
substrate (or the lack thereof) and any significant structural changes
that accompany substrate binding. Significant meaning those changes that
can be reliably determined at the lower resolution. For most of the
structure that may mean you are best off by simply taking the
rigid-body-refined coordinates of the higher resolution structure
without further refinement. I see no problem in doing so and as long as
interesting differences between the structures can be clearly defined
and the procedure is explicity described in publications this should be
perfectly reasonable.
Bart
Edward A Berry wrote:
> You have a good point there and I would be interested in hearing
> some other opinions, so I take the liberty of reposting-
>
> My instinctive preference is that each structure should be
> supported solely by the data that is deposited with it -
> (one dataset one structure) but in terms of good science
> we want to produce the best model we can, and that might be
> the rigid-body-located structure from another dataset.
> In particular the density for the ligand might be clearer
> before overfitting with the low resolution data.
>
> Even if the free-R set is not preserved for the new crystal,
> R and R-free tend to diverge rapidly once any kind of
> fitting with a low data/param is performed, so I think
> the new structure must not have been refined much beyond
> rigid body (and over-all B which is included in any kind
> of refinement). And that choice may be well justified.
> Ed
>
> cdekker wrote:
>
>> Hi,
>>
>> Your reply to the ccp4bb has confused me a bit. I am currently
>> refining a low res structure and realise that I don't know what to
>> expect for final R and Rfree - it is definitely not what most people
>> would publish. So the absolute values of R and Rfree are not telling
>> me much, the only gauge I have is that as long as both R and Rfree are
>> decreasing I am improving the model (and yes, at the moment that is
>> only rigid body refinement).
>> In your email reply you suggest that even though a refinement to
>> convergence that will lead to an increased Rfree (and lower R? - a
>> classic case of overfitting!) would be a better model than the
>> rigid-body-refined only model. This is what confuses me.
>> I can see your reasoning that starting with an atomic model to solve
>> low-res data can lead to this behaviour, but then should the solution
>> not be a modification of the starting model (maybe high B-factors?) to
>> compensate for the difference in resolution of model and data?
>>
>> Carien
>>
>> On 4 Jun 2007, at 19:38, Edward A Berry wrote:
>>
>>> Ibrahim M. Moustafa wrote:
>>>
>>>> The last question: In the same paper, for the complex structure R
>>>> and Rfree are equal (30%) is that an indication for improper
>>>> refinement in these published structure? I'd love to hear your
>>>> comments on that too.
>>>
>>> Several times I solved low resolution structures using high resolution
>>> models, and noticed that R-free increased during atomic positional
>>> refinement. This could be expected from the assertion that after
>>> refinement to convergence, the final values should not depend on
>>> the starting point: If I had started with a crude model and refined
>>> against low resolution data, Rfree would not have gone as low as the
>>> high-resolution model, so if I start with the high resolution model
>>> and refine, Rfree should worsen to the same value as the structure
>>> converges to the same point.
>>>
>>> Thinking about the main purpose of the Rfree statistic, in a very
>>> real way this tells me that the model was better before this step
>>> of refinement, and it would be better to omit the minimization step.
>>> Perhaps this is what the authors did.
>>>
>>> On the other hand it does not seem quite right submit a model that
>>> has simply been rigid-body-refined against the data- I would prefer to
>>> refine to convergence and submit the best model that can be supported
>>> by the data alone, rather than a better model which is really the model
>>> from a better dataset repositioned in the new crystal.
>>>
>>> Ed
>>
>>
>>
>> The Institute of Cancer Research: Royal Cancer Hospital, a charitable
>> Company Limited by Guarantee, Registered in England under Company No.
>> 534147 with its Registered Office at 123 Old Brompton Road, London SW7
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>>
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>
>
>
--
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Bart Hazes (Assistant Professor)
Dept. of Medical Microbiology & Immunology
University of Alberta
1-15 Medical Sciences Building
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Canada, T6G 2H7
phone: 1-780-492-0042
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