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 ----- Original Message ----- From: "Bernhard Rupp (Hofkristallrat a.D.)" <hofkristall...@gmail.com> To: "Michael Thompson" <mi...@chem.ucla.edu>, CCP4BB@JISCMAIL.AC.UK Sent: Monday, March 12, 2012 12:48:42 PM GMT -08:00 US/Canada Pacific Subject: RE: [ccp4bb] Matthews coeff. from model > 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 -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 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. >> > - -- 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/ iD8DBQFPXjthUxlJ7aRr7hoRAqPSAJ0Zr7H/Zt0w8TnaJvHsc5g5mZbZngCcCTEC inwbgapeZ+O0jfc20pMVS/M= =0cVz -----END PGP SIGNATURE----- -- Michael C. Thompson Graduate Student Biochemistry & Molecular Biology Division Department of Chemistry & Biochemistry University of California, Los Angeles mi...@chem.ucla.edu -- Michael C. Thompson Graduate Student Biochemistry & Molecular Biology Division Department of Chemistry & Biochemistry University of California, Los Angeles mi...@chem.ucla.edu
