Dear Sir, The Rw/Rf for P22121 structure solution is ~29/32%. For C2 structure solution, it is a little higher, 32/35%.
With best regards, Sayan Saha. On Fri, Jul 29, 2022 at 3:25 PM Andrew Leslie - MRC LMB < and...@mrc-lmb.cam.ac.uk> wrote: > Dear Sayan, > > Using imosflm, based on the two images that you have > uploaded, the cell appears to be orthorhombic (approx 80, 85, 111) and > there is no evidence for the C2 unit call that you suggested. Using only > the second image there is a C2 solution, but the prediction is very poor > (high positional error). I am therefore a bit surprised that you found a MR > solution in C2. Were the Rfactors that you quoted (29/32%) for the > orthorhombic solution or the C2 solution? > > As Herman pointed out, there is definite streaking in some lunes on image > 2, but this seems to be restricted to a relatively small part of the > diffraction pattern. While this does indicate some kind of disorder, I do > not think this is serious enough to prevent a reliable structure > determination, but it might account for the slightly high R-factors. > > There is definitely a lot of spot overlap, as the mosaic spread (mosflm > definition) is in the region of 1.5°. The oscillation angle would have to > be 0.3° or less to avoid this spot overlap (determined from the Strategy > option in imosflm). Again, as Kay pointed out, this would lead to higher > then expected R-factors. As this is an image plate detector, I can > understand why you might not be using an oscillation angle of 0.1°, but you > do need to check that the oscillation angle you are using does not give > rise to a lot of spatial overlaps and a smaller oscillation angle will > generally give improved quality data, especially if the background level > is quite high, as it is in your images. > > Best wishes, > > Andrew > > On 29 Jul 2022, at 05:06, Sayan Saha <ssaha43...@gmail.com> wrote: > > 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 > > > ######################################################################## 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/
