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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
On 03/12/2012 08:48 PM, Bernhard Rupp (Hofkristallrat a.D.) wrote:
>> 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
>
> ----- Original Message -----
> From: "Tim Gruene" <[log in to unmask]>
> To: [log in to unmask]
> Sent: Monday, March 12, 2012 11:07:29 AM GMT -08:00 US/Canada Pacific
> Subject: Re: [ccp4bb] Matthews coeff. from model
>
> 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
>
> On 03/12/2012 06:35 PM, james09 pruza wrote:
>> Dear CCP4bbers,
>>>
>>> Is there any tool to calculate the Matthews coefficient from a
>>> crystallographic model of RNA-protein complex?
>>>
>>> Thanking you.
>>> James.
>>>
>
>
- --
Michael C. Thompson
Graduate Student
Biochemistry & Molecular Biology Division
Department of Chemistry & Biochemistry
University of California, Los Angeles
[log in to unmask]
- --
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
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