Dear Community,
I work on a crystal structure of a trimeric protein with a total mass of 191
kDa. Data resolution is 2.4A. Protein crystallizes in the presence of 800 mM
ZnSO4, and, as a result, contains above 40 zinc ions attached to the protein
molecule. Certain ions are diffused and/or partially substitutes by water
molecules; the consistency between diffused/water exchanged NCS related zinc
residues is limited. Anomalous map does not provide much help for these poorly
defined sites either.
However, they have to be modeled properly. The best option to model these sites
is to split them into alternative conformations and place accordingly to
chemical environment. But as soon as I split a given Zn residue and attempted
to real space refine its parts in linear mode the Coot prompts “No restrains
found” error message. Sphere refinement does the job… by putting alt confs
together, basically overlaying them. For alt confs of often occurring residues
like Na, Cl, Mg real space refinement works fine in the linear mode, whereas in
sphere mode it acts as for Zn – overlays alt confs.
Is there a way to make Coot understand and refine alt confs of Zn or any other
rare occurring residues? Making refinement operational in linear and sphere
mode would be a great advantage.
Another case is Phenix. ReadySet optimizes geometry and creates restrains only
for part A of a Zn residue, ignoring part B. Same happens with Phenix.refine.
Obviously, occupancy refinement for Zn residue parts does not take place.
And the last, but very important. Sphere refinement in Coot becomes very useful
when treating my Zn sites. However, I wonder where spatial restrains come from?
Any library like ReadySet uses? mon_lib_list.cif contains restrains only for
Zn-Cys bond. Restrains, generated by ReadySet cannot be used in Coot.
I run Coot 0.8.8-pre, Phenix 1.11.1-2575 on Ubuntu 16.04 LTS
Here is an example of such a site. [email protected], [email protected],
[email protected] (yes, anomap is helpful for this site)
https://dl.dropboxusercontent.com/u/32683446/Disordered_Zn_site.png
Thank you,
Sergii Buth, PhD
Postdoctoral Fellow
University of Texas Medical Branch
Department of Biochemistry and Molecular Biology
301 University Blvd.
5.106 Basic Science Bldg.
Galveston, Texas 77555-0647
P 409-772-6332
