Dear Sayan, On Thu, 28 Jul 2022 15:12:30 +0530, Sayan Saha <ssaha43...@gmail.com> wrote:
>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. spot overlap results in inaccurate intensity values. Inaccurate intensities result in high Rwork/Rfree. Why do the spots overlap? High mosaicity? Detector distance too small? Oscillation range too high (0.1° is typically adequate)? It would be good to see the data, otherwise we can only speculate. Space group does not change from one frame to the next. If you use XDS, a good guide to decide between higher and lower-symmetry space groups is to compare their ISa values. best, Kay > >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 > >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/ > ######################################################################## 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/
