Re: [ccp4bb] difference density ripples around Hg atoms

- Protein crystallography

Main steps:

- Protein purification
- Crystallisation

Special:

- Programs for crystallography
- X-ray detectors

Basic tutorials:

   - Chemistry
   - Protein
   - Peptide
   - Amino Acids

Xtal community:

- CCP4BB

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: difference density ripples around Hg atoms
From: Kevin Jude kjude {- at -} BERKELEY {- dot -} EDU
Date: 2007-08-01

Next message:
Subject: Re: pdb-l: Stop the new PDB format!
From: Joe Krahn krahn {- at -} NIEHS {- dot -} NIH {- dot -} GOV
Date: 2007-08-01

Subject: Re: difference density ripples around Hg atoms
From: James Holton JMHolton {- at -} LBL {- dot -} GOV
Date: 2007-08-01

If you are refining against data from near the Hg edge (1.01 A), then
you are most likely using an inappropriate scattering factor for Hg. At
the edge, as much as 25% of the electrons are "missing" (scattering out
of phase). As GMS pointed out, there could also be radiation damage,
which means that the Hg atom could be migrating somewhere else (as in
Ramagopal 2005), also making the occupancy less than 1.0.

You can "soak up" a significant amount of missing electrons with a
B-factor, but not completely. B-factors do not change the total number
of electrons in the atom, so refining just a B when the "true" occupancy
less than 1.0 will match up the peak heights (where the signal is
strong) at the expense of the "tails" (where the "signal" is weaker).
This will result in a modeled atomic shape that is "too fat", giving you
negative ripples in an Fo-Fc map around the atom.

I second GMS's suggestion to refine the occupancy. If your refinement
program does not have such an option, then you can do it manually:
refine a series of models with different Hg occupancies and see which
one minimizes the ripples. If that doesn't work, then try anisotropic B
refinement. Both radiation damage and anomalous scattering polarization
effects can also give ripples around heavy atoms, which you can
kinda-sorta model with an anisotropic B.

-James Holton
MAD Scientist

Klemens Wild wrote:
> Dear friends of the Fourier transform,
>
> I am refining a structure with 2 adjacent Hg atoms bound to cysteines
> of different monomers in the crystal contacts, which means I need to
> refine them as well. While the structure nicely refines (2.2 A data),
> I do not get rid of negative density ripple layers next to them (-10
> sigmas). My question: is this likely due to anistropy of the soft
> mercury atoms (anisotropic B refinement decreases the ripples) or is
> this likely a summation truncation effect prominent for heavy atoms?
> Can I just anistropically refine the mercuries while I keep the rest
> isotropic? Never saw this in a PDB. Suggestions are very welcome.
>
> Greetings
>
> Klemens Wild

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: difference density ripples around Hg atoms
From: Kevin Jude kjude {- at -} BERKELEY {- dot -} EDU
Date: 2007-08-01

Next message:
Subject: Re: pdb-l: Stop the new PDB format!
From: Joe Krahn krahn {- at -} NIEHS {- dot -} NIH {- dot -} GOV
Date: 2007-08-01