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 <[email protected]> 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 <[email protected]> em nome de Kennedy, > Michael <[email protected]> > *Enviado:* quinta-feira, 27 de fevereiro de 2025 19:57 > *Para:* [email protected] <[email protected]> > *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: [email protected] > 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 > > ------------------------------ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > ------------------------------ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
