Matthews coeff. from model

From: james09 pruza
Date: 12 March 2012 17:35

Dear CCP4bbers,

Is there any tool to calculate the Matthews coefficient from a crystallographic model of RNA-protein complex? 

Thanking you.

James.

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From: Tim Gruene

Dear James,

I do not know such a tool, but you can use 140A^3/a.a. and 380A^3/base
to calculate the solvent content by hand.

Regards,
Tim

- --
Dr Tim Gruene

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From: Ian Tickle


matthews_coef ?

-- Ian

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From: Ian Tickle


... or rwcontents ?

-- Ian

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From: Michael Thompson


James,

For a detailed analysis of Matthews coefficients (Matthews probabilities), you can use this web-based tool:

http://www.ruppweb.org/Mattprob/

There is a pull-down menu to select the sample type, and one choice is "protein-DNA complex." Perhaps someone can correct me if I'm wrong, but I can't imagine the results would be very different for protein-DNA vs. protein-RNA.

Also, if you already have a crystallographic model, as you say you do, then you know how many molecules are in the ASU and you could calculate it by hand :

Vm = (volume of unit cell)/(molecular weight of all unit cell contents)

Good luck,

Mike

Dear James,

I do not know such a tool, but you can use 140A^3/a.a. and 380A^3/base
to calculate the solvent content by hand.

Regards,
Tim

--
Michael 

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From: Bernhard Rupp (Hofkristallrat a.D.)

> I can't imagine the results would be very different for protein-DNA vs. protein-RNA.

The reason protein-nucleic acids is an extra category in mattprob is largely due to poorer statistics
resulting from limited sample size and hence no reliable resolution dependence can be computed.

In addition the partial specific volumes for protein (0.74 cm3/g) and nucleic acids (0.50 cm3/g) are
different, so an exact calculation needs to consider their ratio to obtain the correct psv estimate

BR

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From: Michael Thompson


Is there a difference in the psv between DNA and RNA? I assumed (possibly incorrectly) that they would be very close if not exactly the same? Is mattprob more applicable to protein-DNA complexes than Protein-RNA complexes?

Thanks for the insight,

Mike

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From: Tim Gruene 

The number 380A^3/base I gave results from a decent number of nucleic
acids-only PDB files I once analysed with the 'volume' program from
ccp4. I cannot think of an application where knowing the solvent content
must be known to more than 1%, so I bet this number is fine for any such
purposes.

I got the number 140A^3/a.a. from George Sheldrick who told me where he
got this number from, but I do not remember for sure - it could be Kevin
Cowtan, but George may update my memory in order to pay proper credit.

Cheers,
Tim

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From: George Sheldrick


My memory is not as good as it used to be, but I think that I indeed got the number of 140 cubic Angstroms per amino-acid from Kevin. It has worked fine ever since, and is how hkl2map calculates the solvent content for proteins.

George

 

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From: Eleanor Dodson


rwcontents xyzin my.pdb

Eleanor

It will not be able to guess the number og H atoms associated with the RNA so the answer will be a bit out.

Eleanor

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