Dear Sir, image1.osc <https://drive.google.com/file/d/1K5hhoMymVyidOjZyR5Hbfb8ny-KkMIm6/view?usp=drive_web> image2.osc <https://drive.google.com/file/d/16TsGwBPtrkVxOYN7M5PxvJyS0pvMljVZ/view?usp=drive_web> The detector-to-crystal distance was 190 mm. The Oscillation range was 1.0 degree. Please find attached two diffraction images. With best regards, Sayan Saha.
On Thu, Jul 28, 2022 at 9:41 PM Sayan Saha <ssaha43...@gmail.com> wrote: > Dear Sir, > > The detector-to-crystal distance was 190 mm. The Oscillation range was 1.0 > degree. Please find attached two diffraction images. > With best regards, > Sayan Saha. > > > On Thu, Jul 28, 2022 at 7:31 PM Kay Diederichs < > kay.diederi...@uni-konstanz.de> wrote: > >> 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/ >> > ######################################################################## 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/
