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.
Below are a few publications from our lab that cover these topics:
Characterizing metal-binding sites in proteins with X-ray crystallography.
Nat Protoc 13: 1062-1090. [DOI:10.1038/nprot.2018.018] [Pub Med ID:
29674755]
CheckMyMetal: a macromolecular metal-binding validation tool.
Acta Crystallogr D Struct Biol 73: 223-233.
[DOI:10.1107/S2059798317001061] [Pub Med ID: 28291757]
Validation of metal-binding sites in macromolecular structures with the
CheckMyMetal web server.
Nat Protoc 9: 156-70. [DOI:10.1038/nprot.2013.172] [Pub Med ID: 24356774]
Best,
Ivan
With best regards,
Ivan Shabalin, Ph.D.
Research Scientist,
Department of Molecular Physiology and Biological Physics,
University of Virginia,
1340 Jefferson Park Avenue, Pinn Hall,Room 4223,
Charlottesville, VA 22908
https://www.linkedin.com/in/shabalinig/
https://minorlab.org/person/ivan_s/
On 1/21/20 12:55, Chris Fage wrote:
Dear CCP4BB Users,
I've recently solved the ~2.2 angstrom structure of a protein. In my
electron density there are unusual monomer-monomer interfaces involving
pairs of His and Cys residues (see https://ibb.co/wdWBcdk). Note the
positive Fo-Fc density between the four side chains. As there is not
adequate space for a water molecule or metal ion, perhaps the Cys
residues are partially tied up disulfide bonds? However, the
protein looks to be fully monomeric based on LC-MS measurements. Has
anyone else observed crystal-driven formation of disulfide bridges?
Aside from this region, there is no extensive interface between
momoners, and PDBePISA suggests a monomeric state.
Thanks in advance for any advice!
Best wishes,
Chris
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