[ccp4bb] AW: [ccp4bb] Regarding the correct space group identification

2022-07-29 Thread Schreuder, Herman /DE 
Dear Sayan,

There are no multiple diffraction patterns in the images you sent us. However, 
the mosaicity appears to be quite high and in this case I would really 
recommend to process the data with XDS (if you have not already done that).

In the left side of image 2, there appear to be alternating loons with strong 
single spots, and loons with rows of streaky spots which are very close 
together, which reminds me of a crystal with lattice translocation disorder I 
once struggled with. However, it might also be bona fide diffraction, with the 
streaky spots caused by a combination of your long cell axis with high 
mosaicity.

You can check this by overlaying the predicted spots on your diffraction 
pattern. All data processing programs have an option to do this.

Finally, I would superimpose your MR solutions of C2 and P222 and look if they 
are exactly the same. If they are different, e.g. if one of the subunits in one 
of the space groups is translated with respect to the other, your crystal may 
contain a mixture both, causing to problems you are facing.

Best,
Herman



Von: CCP4 bulletin board  Im Auftrag von Sayan Saha
Gesendet: Donnerstag, 28. Juli 2022 18:12
An: CCP4BB@JISCMAIL.AC.UK
Betreff: Re: [ccp4bb] Regarding the correct space group identification

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 
mailto:kay.diederi...@uni-konstanz.de>> wrote:
Dear Sayan,

On Thu, 28 Jul 2022 15:12:30 +0530, Sayan Saha 
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> 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 
>> mailto: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:
>>

Re: [ccp4bb] AW: [ccp4bb] Regarding the correct space group identification

2022-07-28 Thread Sayan Saha 
Dear Madam,

The data were processed in C2 and P222 independently from the same
diffraction. There are two protomers in the ASU.

With best regards,
Sayan Saha.



On Thu, Jul 28, 2022 at 7:25 PM Eleanor Dodson <
176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote:

> I cant see how the C2 cell can be reindexed to the P/mmm one?
> Am I right to assume these are different processing of the same
> diffraction?
> And how many molecules do you have in each cell?
> Eleanor
>
>
>
> On Thu, 28 Jul 2022 at 12:52, Schreuder, Herman /DE <
> herman.schreu...@sanofi.com> wrote:
>
>> Dear Sayan,
>>
>>
>>
>> Thank you for this information. Why are your spots overlapping? The axes
>> of your crystal are not particularly long. Did you put the detector very
>> close to the crystal, or are there multiple diffraction patterns?
>>
>>
>>
>> Did you run Zanuda on your P1 structure? What Rfactors do you get when
>> you complete the refinement in P1?
>>
>>
>>
>> Best regards,
>>
>> Herman
>>
>>
>>
>> *Von:* Sayan Saha 
>> *Gesendet:* Donnerstag, 28. Juli 2022 11:43
>> *An:* Schreuder, Herman /DE 
>> *Cc:* CCP4BB@JISCMAIL.AC.UK
>> *Betreff:* Re: [ccp4bb] Regarding the correct space group identification
>>
>>
>>
>> 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.
>>
>>
>>
>> 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  *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=1
>>
>>
>> --
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>



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Re: [ccp4bb] AW: [ccp4bb] Regarding the correct space group identification

2022-07-28 Thread Eleanor Dodson 
I cant see how the C2 cell can be reindexed to the P/mmm one?
Am I right to assume these are different processing of the same
diffraction?
And how many molecules do you have in each cell?
Eleanor



On Thu, 28 Jul 2022 at 12:52, Schreuder, Herman /DE <
herman.schreu...@sanofi.com> wrote:

> Dear Sayan,
>
>
>
> Thank you for this information. Why are your spots overlapping? The axes
> of your crystal are not particularly long. Did you put the detector very
> close to the crystal, or are there multiple diffraction patterns?
>
>
>
> Did you run Zanuda on your P1 structure? What Rfactors do you get when you
> complete the refinement in P1?
>
>
>
> Best regards,
>
> Herman
>
>
>
> *Von:* Sayan Saha 
> *Gesendet:* Donnerstag, 28. Juli 2022 11:43
> *An:* Schreuder, Herman /DE 
> *Cc:* CCP4BB@JISCMAIL.AC.UK
> *Betreff:* Re: [ccp4bb] Regarding the correct space group identification
>
>
>
> 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.
>
>
>
> 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  *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=1
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>



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[ccp4bb] AW: [ccp4bb] Regarding the correct space group identification

2022-07-28 Thread Schreuder, Herman /DE 
Dear Sayan,

your options left, as far as I can see, are:

- check if your structure is not twinned, or if not, correct for twinning
- refine using the Zanuda space group.
- try to find a better crystal that does not produce multiple diffraction 
images.

Best,
Herman

Von: Sayan Saha 
Gesendet: Donnerstag, 28. Juli 2022 15:17
An: Schreuder, Herman /DE 
Cc: CCP4BB@JISCMAIL.AC.UK
Betreff: Re: [ccp4bb] Regarding the correct space group identification

Dear Sir,
 The crystal-to-detector distance was set to 190 mm. Yes, multiple diffractions 
seem to be present. We have not yet tried Zanuda on the P1 structure. However, 
the Rw/Rf of P1 structures are little higher (31/34%).

With best regards,
Sayan Saha.

On Thu, Jul 28, 2022 at 5:22 PM Schreuder, Herman /DE 
mailto:herman.schreu...@sanofi.com>> wrote:
Dear Sayan,

Thank you for this information. Why are your spots overlapping? The axes of 
your crystal are not particularly long. Did you put the detector very close to 
the crystal, or are there multiple diffraction patterns?

Did you run Zanuda on your P1 structure? What Rfactors do you get when you 
complete the refinement in P1?

Best regards,
Herman

Von: Sayan Saha mailto:ssaha43...@gmail.com>>
Gesendet: Donnerstag, 28. Juli 2022 11:43
An: Schreuder, Herman /DE 
mailto:herman.schreu...@sanofi.com>>
Cc: CCP4BB@JISCMAIL.AC.UK
Betreff: Re: [ccp4bb] Regarding the correct space group identification

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.

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 
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 mailto: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.




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[ccp4bb] AW: [ccp4bb] Regarding the correct space group identification

2022-07-28 Thread Schreuder, Herman /DE 
Dear Sayan,

Thank you for this information. Why are your spots overlapping? The axes of 
your crystal are not particularly long. Did you put the detector very close to 
the crystal, or are there multiple diffraction patterns?

Did you run Zanuda on your P1 structure? What Rfactors do you get when you 
complete the refinement in P1?

Best regards,
Herman

Von: Sayan Saha 
Gesendet: Donnerstag, 28. Juli 2022 11:43
An: Schreuder, Herman /DE 
Cc: CCP4BB@JISCMAIL.AC.UK
Betreff: Re: [ccp4bb] Regarding the correct space group identification

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.

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 
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 mailto: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=1



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[ccp4bb] AW: [ccp4bb] Regarding the correct space group identification

2022-07-28 Thread Schreuder, Herman /DE 
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  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.




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https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1



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