Dear Sayan, your options left, as far as I can see, are:
- check if your structure is not twinned, or if not, correct for twinning - refine using the Zanuda space group. - try to find a better crystal that does not produce multiple diffraction images. Best, Herman Von: Sayan Saha <ssaha43...@gmail.com> Gesendet: Donnerstag, 28. Juli 2022 15:17 An: Schreuder, Herman /DE <herman.schreu...@sanofi.com> Cc: CCP4BB@JISCMAIL.AC.UK Betreff: Re: [ccp4bb] Regarding the correct space group identification Dear Sir, The crystal-to-detector distance was set to 190 mm. Yes, multiple diffractions seem to be present. We have not yet tried Zanuda on the P1 structure. However, the Rw/Rf of P1 structures are little higher (31/34%). With best regards, Sayan Saha. On Thu, Jul 28, 2022 at 5:22 PM Schreuder, Herman /DE <herman.schreu...@sanofi.com<mailto: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<mailto:ssaha43...@gmail.com>> Gesendet: Donnerstag, 28. Juli 2022 11:43 An: Schreuder, Herman /DE <herman.schreu...@sanofi.com<mailto:herman.schreu...@sanofi.com>> Cc: CCP4BB@JISCMAIL.AC.UK<mailto: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<mailto: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<mailto:CCP4BB@JISCMAIL.AC.UK>> Im Auftrag von Sayan Saha Gesendet: Donnerstag, 28. Juli 2022 08:15 An: CCP4BB@JISCMAIL.AC.UK<mailto: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<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/
