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CCP4BB  January 2007

CCP4BB January 2007

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Subject:

Re: advice

From:

"Ohren, Jeffrey" <[log in to unmask]>

Reply-To:

CCP4 bulletin board <[log in to unmask]>

Date:

Mon, 22 Jan 2007 20:59:21 -0500

Content-Type:

text/plain

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text/plain (93 lines)

A follow up to this (for what it's worth) is that it's sometimes easier
to solve a structure by MR from a homologous structure determined by
experimental phases than it is to solve the initial structure by SeMet,
MIR, etc.

An example is the case of the structure determination of the second
isoform of aspartate beta-semialdehyde dehydrogenase from Vibrio
cholerae (vcASADH2). We had 2 Angstrom data and three molecules in the
asu with <30% seq id to the previously determined structures and tried
MR for quite a while without success. Then we made very slow progress
with SeMet and other derivatives for much longer than I would like to
admit.

Once we decided to switch to the Methanococcus jannaschii ortholog (~40%
seq. id to the vcASDAH2) we made much better progress. The structure of
the MjASADH SeMet derivative was determined in a matter of weeks
(Faehnle et al JMB '05) and the structure of the vcASADH2 ortholog was
determined shortly thereafter (publication forthcoming).

In the age of ultra-rapid MolBiol, evaluating other orthologs or
constructs may be faster than sweating over a single construct.

Jeff



-----Original Message-----
From: CCP4 bulletin board [mailto:[log in to unmask]] On Behalf Of
Bart Hazes
Sent: Monday, January 22, 2007 8:08 PM
To: [log in to unmask]
Subject: Re: advice

I'd like to add that the value of a molecular replacement solution tends

to be inversely correlated with the effort needed to find the solution. 
In other words, the harder you have to work to find the MR solution the 
less informative the phase information you tend to get. When you have 
very high resolution and/or NCS you may still be able to solve the 
structure. However, in cases were the search model is only distantly 
related to the protein of interest and Phaser can't find the solution, 
the solution may not be worth finding and you're better of focussing on 
getting experimental phases.

Bart

Randy J. Read wrote:

> On Jan 22 2007, Eaton Lattman wrote:
>
>> Will someone knowledgeable tell me what the present state of full 6  
>> dimensional searches in molecular replacement?
>
>
> Presumably you're referring to systematic 6D searches, not stochastic 
> ones like in EPMR or QoS. Do you mean "can it be done on current 
> hardware" or "is it worth doing"? If the former, then it's doable, 
> though slow. In Phaser, for instance, you can generate a complete list

> of rotations (using the fast rotation function with keywords to 
> prevent clustering and to save all solutions), then feed that big list

> of rotations to the fast translation search. In a typical problem that

> would probably run on a single processor in significantly less time 
> than the average PhD, and could be made reasonably quick with a
cluster.
>
> If the latter, our feeling is that it isn't worth it. We've tried the 
> full search option on a couple of monoclinic problems (where it's only

> a 5D search), and nothing came up with the full list of orientations 
> that didn't come up with the first hundred or so orientations.
>
> We conclude that, even in the most recalcitrant cases, the rotation 
> search gives a better than random indication of whether an orientation

> is correct, so it's not necessary to search through all possible 
> orientations. However, we do feel that it can be worthwhile to try a 
> reasonably large number of orientations in difficult cases.
>
> Best regards,
>
> Randy Read
>
> P.S. When we generate our list of orientations, we use "Lattman" 
> angles to get reasonably even sampling of rotations.
>

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