Chris,
Let me add my five cents to the discussion.
Processing your data to keep I+ and I- merged separately is a very good
practice, as noted by Eleanor and Mitch.
Also, I highly recommend using the CMM server
(https://csgid.org/csgid/metal_sites/) to validate the correctness of
the metal.
When the JCSG was in production, we would routinely collect X-ray emission
spectra from our samples to look for metals. We also saved all crystals
after data collection and if we saw extra anomalous peaks in the maps
during refinement, we would put the crystal up again and collect
quick low
Many thanks for all of the suggestions. Ni2+ or Zn2+ seem to be the most
likely culprits, but I plan to carry out a fluorescence scan at my next
beam session.
While it’s interesting that others have observed crystallization-driven
formation of disulfides, the binding of a metal ion at the given
This conversation brings up the question of whether it would be good practice
to always do a fluorescence scan of a crystal sample, whether it is known to be
a metalloprotein or not...
Energy dispersive X-ray fluorescence spectra (accessible at most synchrotron
sources at this point) can often
Hi Chris,
it could be all Ni besides Zn. I've seen Ni carried over from the initial
metal affinity chromatography I presume.
Cheers Christian
Chris Fage schrieb am Di., 21. Jan. 2020, 21:23:
> Thanks to Guenter and Eleanor for their replies. I mentioned that there is
> not adequate space for
anuary 2020 at 2:06 am
To: "CCP4BB@JISCMAIL.AC.UK"
Subject: Re: [ccp4bb] Unusual monomer-monomer interface in crystal
Dear Chris, are there any metal ions in your buffer or in your protein. We had
a similar looking case. A Zn2+ ion bridged two monomers. Our protein is a Zn2+
binding
As long as you have processed your data to keep I+ and I- meged
separately - default for all CCP4 style data processing it is trivial to do
an anom diff map - see CCP4I2 refinement or other procedures. - Usually the
S show up in this map and give you a scale for peak height.
Then IF you have a
Chris,
We observed electron density for an intermolecular disulfide bond in a protein
that appears to be monomeric in solution.
See Cys166 in 4DSG or 4DSH.
https://www.ncbi.nlm.nih.gov/pubmed/22646091
Jack
John J. Tanner
Professor of Biochemistry and Chemistry
Associate Chair of Biochemistry
Thanks to Guenter and Eleanor for their replies. I mentioned that there is
not adequate space for a metal ion at the described interfaces.
Nevertheless, placement of a metal ion, followed by refinement in Phenix,
repositions the side chains significantly so as to make room for the ion
without
It looks pretty metallic. It would be good to know the max peak height in rms for the difference map and also some of the distances between the His and Cys side chains. Are your sulphur occupancies alright ;-?On 21 Jan 2020 17:55, Chris Fage wrote:Dear CCP4BB Users,I've recently solved the ~2.2
Easy to check whether it is a metal by looking at an anomalous difference
map..
But there are examples of di-sulphides formed between symmetry related
molecules..
Query the wwwpdb -
On Tue, 21 Jan 2020 at 18:06, Guenter Fritz <
guenter.fritz.phenix.c...@gmail.com> wrote:
> Dear Chris, are there
Dear Chris, are there any metal ions in your buffer or in your protein.
We had a similar looking case. A Zn2+ ion bridged two monomers. Our
protein is a Zn2+ binding protein. The Zn2+ originated from some
denatured protein in the drop. No extra Zn2+ was in the crystallization
buffer.
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