[phenixbb] Off-topic: Hydrogen images

mohamed noor mohamed.noor34 at gmail.com
Tue Apr 21 12:09:43 PDT 2015

Thanks everyone. Pavel, one of the images in your presentation was what I
was looking for.

A summary regarding my second question - soaking/exchange can be used if
the crystal is large enough and this is cheaper and faster than
perdeuteration. The latter method is reserved for small crystals. However,
soaking will only exchange labile protons like OH- and not those in CH3 and
CH2. One point mentioned off-board was that growing cells in D2O causes
enough changes such that cells will grow slower and therefore beta lactam
antibiotics like ampicillin is not great.

For those looking for 'special' structures - PDB 4AR3, the really
interesting description of hydronium ion (H3O+) in 3KCJ/3QZA/3QYS
(Kovalevsky et al, Angewandte Chemie 2011) and ultrahigh resolution
structure from neutron data of crambin 4FC1 (thanks Maxime Cuypers and Leif

On Fri, Apr 17, 2015 at 10:58 PM, mohamed noor <mohamed.noor34 at gmail.com>

> Dear all
> I will be presenting about protein crystallography to a group of PhD-level
> physicists and need some images from the community.
> Would anyone have high-quality images of density maps that show hydrogen
> atoms at
> 1. high and ultra-high X-ray resolution (say, about 1.2 A to about 0.5 A)
> 2. low or medium X-ray resolution (where H atoms are not visible) compared
> with neutron data (with H). Ideally these images should be from the same
> protein so that I can show the power of complementary beam source for the
> diffraction.
> A side question - what is the community's preference to get deuterated
> samples? Is it crystal soaking or growing E. coli in deuterium?
> All contributions will be credited. Thanks.
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