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
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
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 crystallogra...@christophmeier.com wrote:
Dear all,
I am refining the X-ray structure of a protein:
Data to ~2A were collected at a latest-generation synchrotron.
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
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
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
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
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...
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,
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?
On Wed, Apr 4, 2012 at 10:31 AM, Roger Rowlett rrowl...@colgate.edu 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
Hi Chris,
As has been suggested already, and seems quite plausible to me, it sounds like
tell-tale signs of radiation damage.
To have little more substance behind this suspicion, some more experimental
details could help:
What was the dose accumulated during data collection?
If the dose cannot
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