Hello Jessica,
options to test (in order to judge what is going on in the active site):
1) Take all the water/ion molecules out of the pocket and refine the
rest of the structure as good as you can (without overfitting
everything) and calculate a sigma A-weighed *3Fo-2Fc* map. Since you
already refined the atoms, there may be some memory effect (if you do
not use the correct/older mtz file), so shake all coordinates/B-factors
a bit before starting the refinement (reset B-factors to 30 and/or
slightly shift the atom coordinates randomly).
2) Consider to use an alternative refinement program (may save the day).
3) Since you have built a model, you can calculate maps on an absolute
scale (i.e. electrons/Å3) - the absence of an atom should result in a
peak of a particular height, but will not be consistent when viewed in
sigma’s.
4) Calculate a "polder" map and/or AK (averaged kicked) map instead of
the classical maps that have there shortcomings.
5) Finally, could be you are facing a partial occupation or alternative
position of a water molecule that will never materialize... You could
spend weeks for little to no progress. In this case, it is better to not
refine anything in that position and write down all your efforts in the
manuscript…..
Cheers,
Jeroen
Am 04.03.20 um 19:04 schrieb Jessica Besaw:
Hey Roger,
I believe the Chloride spot is a negatively changed anion because it
has more density that water and it is close to an arginine. Does this
chloride binding coordination look reasonable?
All of the other water are coordinated to two other side-chains, and
do not depend on the partially occupied water
Cheers!
Jessica
On Wed, 4 Mar 2020 at 12:27, Roger Rowlett <rrowl...@colgate.edu
<mailto:rrowl...@colgate.edu>> wrote:
In addition, one should carefully consider the chemistry and
coordination geometry around the putative chloride ion. Not only
do candidates have to be consistent with the observed omit
density, but they must also make chemical interaction and geometry
sense. I suspect a partial occupancy water may make the most sense
from the limited data provided, but only if all the other placed
solvent molecules have clearly defined interactions that do not
depend solely on the partially occupied water. What does the
chloride coordination geometry look like? Is it clearly a chloride
ion and not a cation?
Roger Rowlett
Gordon & Dorothy Kline Professor, Emeritus
Colgate University
On Wed, Mar 4, 2020, 12:20 PM Nukri Sanishvili <sannu...@gmail.com
<mailto:sannu...@gmail.com>> wrote:
Hi Jessica,
You do not say how well is the rest of the structure refined.
First, you should refine the structure best you can, without
placing anything in the unclear blob of your interest so to
obtain the best possible phases and hopefully improve the blob
density as well.
Then you should let the BB see what that density looks like.
Looking at only the list of possibilities has very little
value without seeing the density itself.
Best wishes,
Nukri
On Wed, Mar 4, 2020 at 11:10 AM Jessica Besaw
<jbesaw1...@gmail.com <mailto:jbesaw1...@gmail.com>> wrote:
Hello friends,
I have a "blob" of density in an active site of my protein.
I am struggling to determine if I should place a water in
this spot, if I should model it as a disordered water, if
the density may be a ligand that I have not considered, or
if it should be left as unaccounted for density. I would
like to publish this structure without compromising the
science.
I have attached several possibilities that I have
considered below.
Any suggestions would be appreciated.
Cheers!
Jessica Besaw
------------------------------------------------------------------------
To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
------------------------------------------------------------------------
To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
------------------------------------------------------------------------
To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
------------------------------------------------------------------------
To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
--
*Dr.math. et dis. nat.Jeroen R. Mesters*
Deputy, Lecturer, Program Coordinator /Infection Biology
/
<http://www.uni-luebeck.de/studium/studiengaenge/infection-biology/introduction.html>Visiting
Professorship (South Bohemian University) in Biophysics
Logo Uni Lübeck
*University of Lübeck*
Center for Structural and Cell Biology in Medicine
*Institute of Biochemistry*
Tel +49 451 3101 3105 (secretariate 3101)
Fax +49 451 3101 3104
jeroen.mest...@uni-luebeck.de <mailto:jeroen.mest...@uni-luebeck.de>
www.biochem.uni-luebeck.de <http://www.biochem.uni-luebeck.de>
*Ratzeburger Allee 160
23538 Lübeck, Schleswig-Holstein
Germany*
########################################################################
To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
