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CCP4BB  September 2017

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Subject:

Re: PAK=0 problem

From:

Rachael Skyner <[log in to unmask]>

Reply-To:

[log in to unmask]

Date:

Fri, 22 Sep 2017 22:16:14 +0000

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I think this is pretty much the reason. Other than the fact that completely different methods are used to solve small molecule vs. macromolecular structures, there are a number of reasons that macromolecular structures aren't as easily/routinely solved. 

A good starting point is to remember exactly what an R2 value tells us. It's an indication of the overall quality of the solution, and does not tell us anything about the quality of local (i.e. regional) refinements. In small molecule structures, the "local refinement" is basically the whole of the asymmetric unit. Providing you get that right, and select the correct space group, you've got the structure. It's pretty straight forward providing there's no twinning or disorder going on, and you know from your experiment what your molecule should look like. 

Macromolecules, on the other hand, are much more anisotropic and don't diffract as well. There's a lot more stuff going on in the diffraction pattern. You're depending on residues behaving like they do in other structures. If just one tiny little bit of the structure behaves unexpectedly, then you can model it wrong, and your solution is done for. (I'm not an expert in macromolecular crystallography, I trained as a small molecule crystallographer... so maybe my reasoning is far too superficial or simplistic)

This is why, in my opinion, other statistical measures should be given their due attention in refinement of macromolecules. As for small molecules, an R2 value is a good general guide of the quality of your solution and refinements, but should not always be taken at face value. Of course, it all depends on what information you actually want from your experiment, too. 

Rachael Skyner
PDRA (XChem)

Diamond Light Source Ltd.
Diamond House, Harwell Science & Innovation Campus, Didcot, Oxfordshire OX11 0DE
Tel: +44(0)1235 56 7537

________________________________________
From: CCP4 bulletin board [[log in to unmask]] on behalf of Tim Gruene [[log in to unmask]]
Sent: 22 September 2017 22:42
To: ccp4bb
Subject: Re: [ccp4bb] PAK=0 problem

Hi James,

small molecule structures usually model every or nearly every atom in the
asymmetric unit - do you think that simple answer is too naive?

Best,
Tim

On Friday, September 15, 2017 9:25:25 AM CEST James Holton wrote:
> You know, I've been pondering that question for most of my adult life.
> Why can't we push macromolecular R factors down to the level of
> experimental error like our "small molecule" colleagues do routinely?  I
> have a few ideas, and others do too.  In fact, there will be session on
> this topic at the next ACA meeting.
>  [...]
> -James Holton
> MAD Scientist
>
> On 9/15/2017 4:32 AM, rohit kumar wrote:
> > why R/Rfree not going down from 21/25?

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Tim Gruene
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phone: +41 (0)56 310 5297

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