This could well be due to radiation damage - S are often affected, also Glu
and Asp side chains. It is hard to know what to do since the effects are
time related. If you have high redundancy maybe you could not use he later
batches? Otherwise maybe just relax the B factor restraints and let them
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Chris
Meier
Sent: Wednesday, April 04, 2012 10:16 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] negative difference density around sulphur and oxygen atoms
Dear all,
I am refining the X-ray structure of a protein:
Data to ~2A
On Wed, Apr 4, 2012 at 10:31 AM, Roger Rowlett wrote:
> I have also seen a recent paper where radiation damage of a bound protein
> ligand was apparently observed in a synchrotron beam.
>
That was a manuscript were I would have happily given the coordinates and
structure factors to the reviewer
could it be that the scattering table would be slightly different for the
sulfur atoms at the collected wavelength?
Are they Cys or Met residues? if Cys is there a possibility of oxidation to the
disulfides?
Dear Chris
Could you please try later version of refmac then if the problem persists
please let me know. Before making any suggestions it would be good to make sure
that the problem is not related with particular software version (as Ian
suggested)
regards
Garib
On 4 Apr 2012, at 16:16, Ch
apart from radation damage it could be a combination of:
- too tight restraints on the B-factors
- 9 sigma not being that much on a the e/A3 scale, i.e. your difference map is
very flat (which is good) and the few peaks that remain stand out a lot, even
if their absolute height is low...
Quot
The PNAS paper you refer to talks about a "loss of definition" of
exposed carboxyl O atoms, i.e. an increase in B factor, but presumably
if this is modelled properly then it shouldn't leave a big hole in the
difference map. After all, the paper is not claiming that C-O bonds
are broken, only that
Hello Chris,
Are you refining individual atomic B factors or grouped? Perhaps the B factors
of the terminal atoms of the side chain are being restrained to too low of a B
factor resulting in excessive negative density?
Scott
On Apr 4, 2012, at 8:16 AM, Chris Meier wrote:
> Dear all,
> I am r
>
> I look forward to hearing from others how best to handle this in
> refinement.
>
>
Dose-dependent occupancies (tau of an exponential decay function?) refined
against unmerged data
JPK
***
Jacob Pearson Keller
Northwestern University
Medical Scientist Tr
Radiation damage induced loss of definition of disulfide bridges, side
chain carboxylates, and certain histidine residues has been observed in
synchrotron-irradiated protein crystals. For example, see Weik et al.,
PNAS 2000, 97, 623. I have also seen a recent paper where radiation
damage of a b
PS you say the model is complete, but just as important how complete
is (are?) the data.
-- Ian
On 4 April 2012 16:16, Chris Meier wrote:
> Dear all,
> I am refining the X-ray structure of a protein:
> Data to ~2A were collected at a latest-generation synchrotron.
> The 2fo-Fc maps are crisp, th
Hi Chris
I would say there's something very wrong if you're seeing -6 sigma
difference peaks at O atoms. I don't see how this can be explained by
radiation damage. I for one have never seen that before in a
structure where there weren't other obvious issues (or maybe I just
haven't looked hard e
Dear all,
I am refining the X-ray structure of a protein:
Data to ~2A were collected at a latest-generation synchrotron.
The 2fo-Fc maps are crisp, the model of the protein is complete and I am
reasonably happy with the stats (R below 20%, Rfree below 25% in Refmac 5.5).
However, I am seeing a lot
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