[3dem] Sample density in CryoEM

[martyn.winn at stfc.ac.uk]

Hi,

Regarding nucleic acids, you may find Kantardjieff and Rupp, "Matthews coefficient probabilities: Improved estimates for unit cell contents of proteins, DNA, and protein–nucleic acid complex crystals", Protein Science 12, 1865-1871 (2003) useful. This is for the Matthews coefficient used in crystallography, which in turn assumes an estimate of the density of the protein or nucleic acid. 
They quote a partial specific volume of nucleic acids of 0.5 cm3 / g, and they cite a couple of older references which may explain the variation (I haven't checked).

HTH
Martyn

> -----Original Message-----
> From: 3dem-bounces at ncmir.ucsd.edu [mailto:3dem-bounces at ncmir.ucsd.edu]
> On Behalf Of Ingvar Lagerstedt
> Sent: 19 September 2012 14:02
> To: 3dem
> Subject: [3dem] Sample density in CryoEM
> 
> Hi,
> I am looking at correlating the volume of a 3D EM reconstruction with
> the theoretical volume of the sample.  To do that I need the density of
> sample.  There are several published values for proteins, see for
> instance http://www.ncbi.nlm.nih.gov/pubmed/10930825, but values for
> nucleic acids are harder to find.  There is also the question what, if
> any, the thermal contraction is when snap-freezing a sample.  It may be
> that any thermal contraction is to small to be noticable, e.g. water
> ice contract about 1.8% from 273 K to 95 K, and I expect the
> uncertainty in the volume calculation to be larger than that.
> 
> By calculating the volume at a series of contour level, I can choose
> the level that is closest to the theoretical volume.  It may be
> necessary to mask out the background noise before calculating.
> 
> Any pointers on this type of calculation appreciated.
> 
> Regards,
> Ingvar
> 
> --
> Ingvar Lagerstedt, PDBe, EMBL-EBI, Hinxton, UK Ingvar at ebi.ac.uk
> 
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