I cant see how the C2 cell can be reindexed to the P/mmm one? Am I right to assume these are different processing of the same diffraction? And how many molecules do you have in each cell? Eleanor
On Thu, 28 Jul 2022 at 12:52, Schreuder, Herman /DE < herman.schreu...@sanofi.com> wrote: > Dear Sayan, > > > > Thank you for this information. Why are your spots overlapping? The axes > of your crystal are not particularly long. Did you put the detector very > close to the crystal, or are there multiple diffraction patterns? > > > > Did you run Zanuda on your P1 structure? What Rfactors do you get when you > complete the refinement in P1? > > > > Best regards, > > Herman > > > > *Von:* Sayan Saha <ssaha43...@gmail.com> > *Gesendet:* Donnerstag, 28. Juli 2022 11:43 > *An:* Schreuder, Herman /DE <herman.schreu...@sanofi.com> > *Cc:* CCP4BB@JISCMAIL.AC.UK > *Betreff:* Re: [ccp4bb] Regarding the correct space group identification > > > > Dear Sir, > > > > 1. There are no ice-rings. However, diffraction spots seem to be > overlapping. This can be seen during the data processing, as the space > group (C2 or P222) varies even in the consecutive frames. > > > > 2. Crystal packing of C2 and P22121 seem to be similar (please see the > attached images). > > > > 3. Forgot to mention in my previous email that we have already processed > the data in P1 and MR solution could be found only in P1 (Phaser was used > with an option in all possible space groups of that point group). > > > > Please let me know if any other information is required. > > > > With best regards, > > Sayan Saha. > > > > > > On Thu, Jul 28, 2022 at 1:26 PM Schreuder, Herman /DE < > herman.schreu...@sanofi.com> wrote: > > Dear Sayan, > > > > If a subunit is correctly oriented, but the translation is incorrect, > density for a ligand may still show up in the binding site of the protein. > It might be that one of the 2-fold axes, you think is crystallographic, is > in fact non crystallographic and a few Angstroms away from the > crystallographic position. > > > > What I would do: > > 1. Check the images: are there ice-rings or other artifacts that could > cause scaling problems that would lead to high Rw/Rf values? In that case, > there is not much you can do. > 2. Compare the C2 and P22121 solutions: do they have the same overall > crystal packing (CS+NCS), or are they different? Do they have the same > Rw/Rf values? Can we learn anything from the differences in overall crystal > packing? > 3. Process, run MR and refine in P1. Do you get lower R-factors? If > so, then run Zanuda to find out the real space group. > > > > Best, > > Herman > > > > *Von:* CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> *Im Auftrag von *Sayan > Saha > *Gesendet:* Donnerstag, 28. Juli 2022 08:15 > *An:* CCP4BB@JISCMAIL.AC.UK > *Betreff:* [ccp4bb] Regarding the correct space group identification > > > > Dear All, > > > > We have collected home-source X-ray intensity data for a protein at 2.6 > Angstrom. The data can be processed in either C2 (a=120, b=80, c=85 and > beta=115) or P222 (P22121, a=80, b=85, c=110). MR solution can be obtained > in both the space groups. However, the solution can be refined with an > Rw/Rf of 29/32% only. The protein is bound to a ligand (co-crystallization) > for which a clear density can be observed. > > > > Any help and suggestion in this regard would be very helpful. > > > > With best regards, > > Sayan Saha. > > > > > ------------------------------ > > 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/
