Agree with Herman except re using refined model as search model. This will almost always return the answer you started from.. Eleanor
On Thu, 1 Apr 2021 at 13:49, Schreuder, Herman /DE < [email protected]> wrote: > Dear Sam, > > > > The first thing that would come to my mind would be ice rings, but since > you said you don’t have them, there must be another reason for the high Rs. > > Zanuda will give you back the space group you used for MR and maybe a > higher symmetry space group, but the program cannot be used to confirm that > the space group you assigned is correct. For that, you will have to run > Phaser with all possible P2x2x2x permutations. I assume you have already > done that. If not, that would be the second thing I would try. You could > even use your rebuild model as a search model. > > > > The next thing would be to look into the ligand you used. If the ligand > has partial occupancy and induces some conformational changes in the > protein, your crystal may contain proteins with a mixture of conformations, > which may also give rise to higher Rfactors. > > > > Good luck, Herman > > > > *Von:* CCP4 bulletin board <[email protected]> *Im Auftrag von *Sam > Tang > *Gesendet:* Donnerstag, 1. April 2021 14:28 > *An:* [email protected] > *Betreff:* [ccp4bb] High Rs > > > > Dear all > > > > I have a dataset processed to 2.2 A, P212121, with no major issues > identified by Xtriage (no tNCS, no twinning, no ice ring, good > completeness). Phaser-MR gave a good solution except some loop regions are > shifted. There is only 1 molecule in the ASU (and seemingly no more > molecule can be accommodated). I fitted the displaced loops, and confirmed > the space group by Zanuda, but the R-factors stuck at 0.34/0.41 range. > What other aspects should I look into? Twin-refinement? (I am a bit > reluctant to do so because neither Xtriage nor Pointless report it is > twinned) I should also point out that the crystal was grown with its ligand > but I cannot see good density for it. > > > > BRs > > > > Sam > > > ------------------------------ > > 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%7C24d0d2227427449212e008d8f509b65b%7Caca3c8d6aa714e1aa10e03572fc58c0b%7C0%7C0%7C637528769783183293%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=%2BGUemqHp%2BwV8Seq84BJCNkej03RQGCwyZBrur66%2FRCQ%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/
