Another idea - you dont mention resolution., but possibly the ligand is very wobbly, and appropriate B values would range widely. Some refinement defaults restrain the whole "residue" B factors quite tightly to a mean value. There are ways to relax Bfactor restraints but you will have to read the manual I guess.. Eleanor
On Tue, 24 Nov 2020 at 12:43, Schreuder, Herman /DE < herman.schreu...@sanofi.com> wrote: > Hi Nika, > > > > Here you need some common sense. The green density in you polder map may > just be the bulk solvent that was removed from the model to generate the > polder map. In this case you have to use common sense and ask yourself a > couple of questions: > > - Is the density really from the ligand, of from some other component > from your crystallization solution? Molecules like tris or hepes love it to > masquerade for ligands of interest. > - Could it be that only part of the ligand is visible because the > other parts are disordered or not present? This happens quite often. > Instead of the full-ligand, a break-down product or reaction intermediate > might have bound, or part of the ligand binding site is occupied by crystal > contact. > > In this case I would fit the part of the ligand which has convincing > electron density, refine and look at the electron density maps to see if > the fit to the density is convincing and if additional atoms could be added > to the ligand. If you cannot fit the whole ligand, even after some efforts, > I would submit a partially fitted model. > > > > Best, > > Herman > > > > > > > > *Von:* CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> *Im Auftrag von *Nika > Žibrat > *Gesendet:* Dienstag, 24. November 2020 12:29 > *An:* CCP4BB@JISCMAIL.AC.UK > *Betreff:* [ccp4bb] phenix.refine with ligand with ambiguous electron > density > > > > Hello, > > > > I have a question about protein-ligand, of which ligand displays an > ambiguous electron density. I am solving a structure of protein with > ligand which was obtained via soaking. Structural characteristics indicate > the ligand is present however the electron density is quite vague and too > small for the size of the whole ligand. I did a Polder map which showed > much larger area of green density. After insertion of my ligand into the > green density in Polder I ran phenix.refine and there is a lot of red on > the spot where the ligand is which was to be expected. This leaves me > wondering how, if even do I incorporate the polder map data into my refine > input. > > > > My question is, how do I continue refining and validating the structure in > this case? > > > > Thank you, > > > > Nika Žibrat > > > > > ------------------------------ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2FWA-JISC.exe%3FSUBED1%3DCCP4BB%26A%3D1&data=04%7C01%7CHerman.Schreuder%40SANOFI.COM%7C56080723579a4530a08008d8906c42c0%7Caca3c8d6aa714e1aa10e03572fc58c0b%7C0%7C1%7C637418142105522594%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=pebjZIXHZMUjaHn7qx55Io7vA%2F2TmW4h4Sgeio38wCs%3D&reserved=0> > > ------------------------------ > > 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/
