Hi Akanksha,
years ago I tried to refine, using refmac, an inhibitor only with
partial occupancy bound to HIV-1 PR and was not that happy (probably a
biased view) with the outcome.
In a next step I included water molecules with partial occupancies that
normally occupy the binding site in the absence of inhibitor but was not
happy at all because especially the water molecules, despite partial
occupancies and total occupancy of both water and inhibitor equal to 1,
shifted to positions deviating from the positions observed in the
uninhibited structure. For a refinement involving the inhibitor only I
can understand some drift of the inhibitor which is related to the
position/density of the partial waters that were not included in the
model......
In a next step I then compared NCS, Refmac and SHELXL refinement with
partial occupancy for inhibitor + waters in the binding site and spend
weeks optimizing the parameters in the different programs.
End of story, SHELX - based on a visual inspection of the final ED maps
- came closest to what I considered acceptable but again, maybe a biased
view (did not test Buster tough!):
What I learned from this "partial occupancy" odyssee:
1) Different programs handled this type of "constellation" differently
2) Including partial waters did make a difference altough it was/is not
common practice
3) Inhibitor occupancy and position drifted somewhat comparing with or
without waters
As already pointed out, you can not have different occupancies for the
different atoms of the ligand. At 2.1 Å resolution, test several fixed
occupancies - start at 0.5 and increase by 0.1 - and compare/inspect the
different ED maps along witht the R/Rfree etc. and pick the occupancy
that makes most sense....
Good luck,
Jeroen
Am 03.03.22 um 16:08 schrieb Wim Burmeister:
Hello,
at 2.1 A resolution, atomic temperature factors and occupancy are
strongly correlated. So you have to be very careful with the results.
So the best is just to set the inhibitor to the average occupancy and
then to include it into a full positional and B-factor refinement. You
can check whether the result is coherent by comparing the B-factors of
the ligand and of the atoms, which are in contact with it. If this is
not the case, you may want to adjust the occupancy manually. As there
are also solvent atoms at the ligand positions, when it is not bound,
there is another source of inaccuracy and theoretically you would have
to model the site with the solvent and an occupancy 1-q and the ligand
with an occupancy q as alternate structures. But nobody does that and
it is not really required.
Best
Wim
------------------------------------------------------------------------
*De: *"Akanksha Tomar" <akankshat...@gmail.com>
*À: *"CCP4BB" <CCP4BB@JISCMAIL.AC.UK>
*Envoyé: *Jeudi 3 Mars 2022 15:15:07
*Objet: *[ccp4bb] Ligand occupancy refinement
Hi everyone,
I am trying to refine the occupancy of a bound ligand. After fixing
the protein model and water I fitted the ligand into it. Currently, I
am using Phenix Refine with occupancy refinement for individual atoms
switched on. After the refinement, the overall occupancy of the ligand
is 0.7 and the RSCC value is 0.86. The resolution of the structure is
2.1 Å.
Now the problem is that the program has assigned different occupancies
to different atoms of the ligand. For some cases, it has assigned 0
occupancies to atoms for which there is a clear positive peak.
Why it has been done so and is it acceptable?
Any help would be greatly appreciated.
Thank you.
--
Best Regards,
Akanksha Tomar
Pre-Doctoral Fellow,
C\o Dr. Arockiasamy Arulandu,
Membrane Protein Biology Group,
International Center for Genetic Engineering and Biotechnology,
New Delhi, India
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*Wim Burmeister*
Professor
Institut de Biologie Structurale (IBS) CIBB
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Mobile: +33 (0) 7 50 49 19 91
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signature.html *Dr. /math. et dis. nat./ Jeroen R. Mesters
*Deputy, Lecturer, Program Coordinator Infection Biology
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