-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 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" <t...@shelx.uni-ac.gwdg.de> > To: CCP4BB@JISCMAIL.AC.UK > 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 mi...@chem.ucla.edu - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.11 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFPXl8gUxlJ7aRr7hoRAnKIAKC9BiLuWTo8j/NOUkKee1FlcOSULACggsPw uFJo7bCPaZ2mJ/LQcsxkDKU= =Wzko -----END PGP SIGNATURE-----
