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
> <mailto: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 <mailto:kay.diederi...@uni-konstanz.de>>
> wrote:
> Dear Sayan,
>
> On Thu, 28 Jul 2022 15:12:30 +0530, Sayan Saha <ssaha43...@gmail.com
> <mailto: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 <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.
> >>
> >>
> >>
> >>
> >> ------------------------------
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