Dear Sayan,
I could be wrong, but perhaps Kay was asking you to provide
the actual images, rather than jpeg images. One can usually get a lot more
information by processing the actual images rather than looking at the jpegs.
Best wishes,
Andrew
> On 28 Jul 2022, at 17:11, Sayan Saha <[email protected]> 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
> <[email protected] <mailto:[email protected]>>
> wrote:
> Dear Sayan,
>
> On Thu, 28 Jul 2022 15:12:30 +0530, Sayan Saha <[email protected]
> <mailto:[email protected]>> 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 <
> >[email protected] <mailto:[email protected]>> 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 <[email protected]
> >> <mailto:[email protected]>> *Im Auftrag von *Sayan
> >> Saha
> >> *Gesendet:* Donnerstag, 28. Juli 2022 08:15
> >> *An:* [email protected] <mailto:[email protected]>
> >> *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.
> >>
> >>
> >>
> >>
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