Hi Pavel,
Interesting! I have always been told that one should include only what could be
seen. In this scenario, I would model hydrogens only if I had a sub 1 A
resolution or if I had Neutron diffraction data. Thanks for the documentation.
All the best
______________________________________________________
Rafael Marques da Silva
PhD Student – Structural Biology
University of Leicester
Mestre em Física Biomolecular
Universidade de São Paulo
Bacharel em Ciências Biológicas
Universidade Federal de São Carlos
phone: +44 07861 273773
"A sorte acompanha uma mente bem treinada"
________________________________________________
________________________________
De: Pavel Afonine <pafon...@gmail.com>
Enviado: domingo, 2 de março de 2025 22:10
Para: Rafael Marques <rafael_mmsi...@hotmail.com>
Cc: CCP4BB@jiscmail.ac.uk <CCP4BB@jiscmail.ac.uk>
Assunto: Re: [ccp4bb] unknown density
Hi Rafael,
Regarding your question about hydrogens: it's a good practice to include them
using the riding model towards the end of refinement, regardless of resolution.
Hydrogens make up about half of the model atoms, contribute to the scattering,
and about 85% of them have geometrically unambiguous positions based on their
parent atoms. Including hydrogens also helps achieve more sensible model
geometry by improving non-covalent interactions and reducing steric clashes.
Some notes related to this:
https://phenix-online.org/phenixwebsite_static/mainsite/files/newsletter/CCN_2012_01.pdf#page=18
All the best,
Pavel
On Sat, Mar 1, 2025 at 8:20 AM Rafael Marques
<rafael_mmsi...@hotmail.com<mailto:rafael_mmsi...@hotmail.com>> wrote:
Hi Michael,
It looks like PEG to me too. Have you used a smaller PEG as cryoprotectant.
Such as PEG 200 or PEG400? Also, as an off topic thing, why are you refining
hydrogens at this resolution?
Best wishes
______________________________________________________
Rafael Marques da Silva
PhD Student – Structural Biology
University of Leicester
Mestre em Física Biomolecular
Universidade de São Paulo
Bacharel em Ciências Biológicas
Universidade Federal de São Carlos
phone: +44 07861 273773
"A sorte acompanha uma mente bem treinada"
________________________________________________
________________________________
De: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>>
em nome de Kennedy, Michael
<michael.kenn...@miamioh.edu<mailto:michael.kenn...@miamioh.edu>>
Enviado: quinta-feira, 27 de fevereiro de 2025 19:57
Para: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>
<CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>>
Assunto: [ccp4bb] unknown density
Hello All,
We recently solved the structure of a protein at 1.8A. There is a large unknown
density (see attached) at the interface between two protein molecules.
The crystallization buffer was 0.2 M Li Sulfate, 0.1 M Tris,25% PEG 4000, 10%
glycerol.
The protein purification buffer was 250 mM NaCl, 20 mM Tris, 10% glycerol, 300
mM imidazole.
Does anyone recognize this ligand or have an idea about what it might be?
thanks
Michael A. Kennedy, PhD
Eminent Scholar and Professor
Department of Chemistry and Biochemistry
106 Hughes Laboratory
Miami University
651 East High Street
Oxford, OH 45056
phone: 513-529-8267
fax: 513-529-5715
email: kenne...@miamioh.edu<mailto:kenne...@miamioh.edu>
webpage: http://chemistry.muohio.edu/kennedy/
google scholars citations:
https://scholar.google.com/citations?user=7rWzfjkAAAAJ
NCBI My Bibliography
https://www.ncbi.nlm.nih.gov/myncbi/1L3_kwfzxCU/bibliography/public/
Lab Twitter : @Kennedy_Lab
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