Re: [ccp4bb] B-factor & Space gr questions!

- Protein crystallography

Main steps:

- Protein purification
- Crystallisation

Special:

- Programs for crystallography
- X-ray detectors

Basic tutorials:

   - Chemistry
   - Protein
   - Peptide
   - Amino Acids

Xtal community:

- CCP4BB

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Scientist or Senior Scientist position available in Plexxikon Inc.
From: Jinyu Liu JinyuLiu {- at -} PLEXXIKON {- dot -} COM
Date: 2007-06-05

Next message:
Subject: Re: B-factor & Space gr questions!
From: Phil Jeffrey pjeffrey {- at -} PRINCETON {- dot -} EDU
Date: 2007-06-05

Subject: Re: B-factor & Space gr questions!
From: Edward A Berry eaberry {- at -} LBL {- dot -} GOV
Date: 2007-06-05

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 3RP.
>
> This e-mail message is confidential and for use by the addressee only.
> If the message is received by anyone other than the addressee, please
> return the message to the sender by replying to it and then delete the
> message from your computer and network.

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Scientist or Senior Scientist position available in Plexxikon Inc.
From: Jinyu Liu JinyuLiu {- at -} PLEXXIKON {- dot -} COM
Date: 2007-06-05

Next message:
Subject: Re: B-factor & Space gr questions!
From: Phil Jeffrey pjeffrey {- at -} PRINCETON {- dot -} EDU
Date: 2007-06-05