Re: [ccp4bb] Unknown electron density

[Alastair MC EWEN]

Hi Betty,


I've seen very similar looking similar looking density from trifluoroacetic 
acid that was present with a synthetic peptide. Could be something to check if 
you have a peptide bound.


Best,

Alastair


~
Alastair McEwen, PhD
Integrated Structural Biology Platform
IGBMC
1 rue Laurent Fries
67404 ILLKIRCH - FRANCE
tel: +33 (0)3 69 48 52 82

From: CCP4 bulletin board  on behalf of Betty Chu 

Sent: 19 April 2023 18:58:53
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Unknown electron density

Dear CCP4BB,

I am working on a structure refinement and came across a blob of density that 
looks like an anvil (see link). Has anyone seen this before and have an idea of 
what it is?


https://drive.google.com/file/d/1BGNwV3MujYjrV4W5m1bh3_WWd49RhJ1w/view?usp=sharing

The protein is in potassium phosphate and the components in the 
crystallization/cryo condition are zinc acetate, PEG, and glycerol.

Thank you in advance for your time and help!

Betty



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] Unknown electron density

[Anat Bashan]

Hi Betty,

You may use the two following applications from the minor lab :
CheckMyMetal - https://cmm.minorlab.org/
CheckMyBlob -  https://cmm.minorlab.org/

Best, Anat.

From: CCP4 bulletin board  On Behalf Of Betty Chu
Sent: Wednesday, 19 April 2023 19:59
To: CCP4BB@jiscmail.ac.uk
Subject: [ccp4bb] Unknown electron density

Dear CCP4BB,

I am working on a structure refinement and came across a blob of density that 
looks like an anvil (see link). Has anyone seen this before and have an idea of 
what it is?


https://drive.google.com/file/d/1BGNwV3MujYjrV4W5m1bh3_WWd49RhJ1w/view?usp=sharing

The protein is in potassium phosphate and the components in the 
crystallization/cryo condition are zinc acetate, PEG, and glycerol.

Thank you in advance for your time and help!

Betty



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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hosted by www.jiscmail.ac.uk, terms & conditions are available at 
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Re: [ccp4bb] Unknown electron density

[David J. Schuller]

Anomalous data might have been helpful. Zinc has an edge at 1.2837 A.


===
 All Things Serve the Beam
 ===
 David J. Schuller
 modern man in a post-modern world
 MacCHESS, Cornell University
 schul...@cornell.edu

From: CCP4 bulletin board  on behalf of Betty Chu 

Sent: Wednesday, April 19, 2023 12:58 PM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: [ccp4bb] Unknown electron density

Dear CCP4BB,

I am working on a structure refinement and came across a blob of density that 
looks like an anvil (see link). Has anyone seen this before and have an idea of 
what it is?


https://drive.google.com/file/d/1BGNwV3MujYjrV4W5m1bh3_WWd49RhJ1w/view?usp=sharing

The protein is in potassium phosphate and the components in the 
crystallization/cryo condition are zinc acetate, PEG, and glycerol.

Thank you in advance for your time and help!

Betty



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

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/

[ccp4bb] Unknown electron density

[Betty Chu]

Dear CCP4BB,

I am working on a structure refinement and came across a blob of density
that looks like an anvil (see link). Has anyone seen this before and have
an idea of what it is?


https://drive.google.com/file/d/1BGNwV3MujYjrV4W5m1bh3_WWd49RhJ1w/view?usp=sharing

The protein is in potassium phosphate and the components in the
crystallization/cryo condition are zinc acetate, PEG, and glycerol.

Thank you in advance for your time and help!

Betty



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=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/

Re: [ccp4bb] Unknown electron density

[Philippe BENAS]

And another question: is the protein known to work with a cofactor that you 
could have kept all along the purification ?
Best regards,Philippe Philippe BENAS, Ph.D.
Dog in the manger
"Un importun survient qui trouble l'intimité, qui arrête l'expansion, qui glace 
le plaisir, - probablement comme un étranger tombant au milieu d'enfants en 
train de danser une ronde", Alfred Delvau, Dictionnaire de la langue verte 
(1866).

Laboratoire de Cristallographie et RMN Biologiques, UMR 8015 CNRS
Faculté de Pharmacie, Université Paris Descartes
Case 48
Av, de l'Observatoire
F-75270 PARIS cedex 06
+33.1.5373.1599
E-mails: philippe.be...@parisdescartes.fr, philippe_be...@yahoo.fr
URLs: http://lcrbw.pharmacie.univ-paris5.fr/ , 
http://lcrbw.pharmacie.univ-paris5.fr/spip.php?article18



  De : Vijaykumar Pillalamarri <vijaypkuma...@gmail.com>
 À : Philippe BENAS <philippe_be...@yahoo.fr> 
Cc : "CCP4BB@JISCMAIL.AC.UK" <CCP4BB@jiscmail.ac.uk>
 Envoyé le : Vendredi 27 octobre 2017 14h08
 Objet : Re: [ccp4bb] Unknown electron density
   
Dear Philippe,
Here is the images showing anomalous map at Co contoured at 5.
Thanks,Vijaykumar
On 27 October 2017 at 14:05, Philippe BENAS <philippe_be...@yahoo.fr> wrote:

Hello Vijaykumar,
Well, 27 e- * 0.4 = 10.8 e- which is very close to 8 (O).In addition I don't 
recognize the expected Co2+ coordination in your structure. I think evidence 
from an anomalous signal would be wellcome. Evidence from another crystal is 
not a proof for this crystal structure. It could be just a little stronger if 
the two crystals come from the same drop.
You can get anomalous info even if the crystal was not collected at the 
wavelength that maximises f". For instance, the crystal for which I provided 
the two snapshots was collected at 0.95 Angst. Not only the anomalous signal is 
well defined for the Co2+ but also for disulfide bridges. Lamdba around 1 
Angst. is a common value for native data collection on synchrotrons so that I'm 
pretty sure you can get such signal from your data.
And a good trick is to always process your data assuming the Friedel Law is not 
respected so that you can get quick access to the anomalous signal in case you 
need it.
HTH,Philippe Philippe BENAS, Ph.D.
Dog in the manger
"Un importun survient qui trouble l'intimité, qui arrête l'expansion, qui glace 
le plaisir, - probablement comme un étranger tombant au milieu d'enfants en 
train de danser une ronde", Alfred Delvau, Dictionnaire de la langue verte 
(1866).

Laboratoire de Cristallographie et RMN Biologiques, UMR 8015 CNRS
Faculté de Pharmacie, Université Paris Descartes
Case 48
Av, de l'Observatoire
F-75270 PARIS cedex 06
+33.1.5373.1599
E-mails: philippe.benas@parisdescartes. fr, philippe_be...@yahoo.fr
URLs: http://lcrbw.pharmacie.univ- paris5.fr/ , http://lcrbw.pharmacie.univ- 
paris5.fr/spip.php?article18



  De : Vijaykumar Pillalamarri <vijaypkuma...@gmail.com>
 À : CCP4BB@JISCMAIL.AC.UK 
 Envoyé le : Vendredi 27 octobre 2017 8h59
 Objet : Re: [ccp4bb] Unknown electron density
   
Dear Dr. Philippe,
There is no symmetry axis nearby the density. I did not computed anomalous map 
for this structure. In this structure, the occupancy of Co is only 0.4 (May be 
because I have added less Co).  We have proved the presence of Co in one of our 
another crystal structure of same protein.
Thanks,Vijaykumar
On 26 October 2017 at 23:11, Philippe BENAS <0d88e888355a-dmarc- 
requ...@jiscmail.ac.uk> wrote:

Dear all and Vijaykumar,
I am personally much more concerned about the Co density which does not seem as 
strong as expected for an atom with Z = 27, aren't you ?

Also I was wondering if there is no symmetry axis around your unkown density. 
Symmetry axes are often a garbage place for all the unexplained density 
everywhere else in the a.u.
Would you have by any chance computed an anomalous map ? It could help for both 
your unknown density and the Co.
Attached is a snapshot of 1.58 Angst. resolution structure showing a 2mFo-DFc 
map in blue and contoured at 2 sigma level as well as an anomalous map 
contoured at 8 sigma (snap1.png). snap2.png shows the 2mFo-DFc at 4 sigma.

Best regards,Philippe Philippe BENAS, Ph.D.
Dog in the manger
"Un importun survient qui trouble l'intimité, qui arrête l'expansion, qui glace 
le plaisir, - probablement comme un étranger tombant au milieu d'enfants en 
train de danser une ronde", Alfred Delvau, Dictionnaire de la langue verte 
(1866).

Laboratoire de Cristallographie et RMN Biologiques, UMR 8015 CNRS
Faculté de Pharmacie, Université Paris Descartes
Case 48
Av, de l'Observatoire
F-75270 PARIS cedex 06
+33.1.5373.1599
E-mails: philippe.benas@parisdescartes. fr, philippe_be...@yahoo.fr
URLs: http://lcrbw.pharmacie.univ- paris5.fr/ , http://lcrbw.pharmacie.univ- 
paris5.fr/spip.php?article18



  De : Nick Pearce <n.m.pea...@uu.nl>
 À : CCP4BB@JISCMAIL.AC.UK 
 Envoyé le 

Re: [ccp4bb] Unknown electron density

[Philippe BENAS]

And did you try SA omit maps ?
Best,
P.
 Philippe BENAS, Ph.D.
Dog in the manger
"Un importun survient qui trouble l'intimité, qui arrête l'expansion, qui glace 
le plaisir, - probablement comme un étranger tombant au milieu d'enfants en 
train de danser une ronde", Alfred Delvau, Dictionnaire de la langue verte 
(1866).

Laboratoire de Cristallographie et RMN Biologiques, UMR 8015 CNRS
Faculté de Pharmacie, Université Paris Descartes
Case 48
Av, de l'Observatoire
F-75270 PARIS cedex 06
+33.1.5373.1599
E-mails: philippe.be...@parisdescartes.fr, philippe_be...@yahoo.fr
URLs: http://lcrbw.pharmacie.univ-paris5.fr/ , 
http://lcrbw.pharmacie.univ-paris5.fr/spip.php?article18



  De : Vijaykumar Pillalamarri <vijaypkuma...@gmail.com>
 À : Philippe BENAS <philippe_be...@yahoo.fr> 
Cc : "CCP4BB@JISCMAIL.AC.UK" <CCP4BB@jiscmail.ac.uk>
 Envoyé le : Vendredi 27 octobre 2017 14h08
 Objet : Re: [ccp4bb] Unknown electron density
   
Dear Philippe,
Here is the images showing anomalous map at Co contoured at 5.
Thanks,Vijaykumar
On 27 October 2017 at 14:05, Philippe BENAS <philippe_be...@yahoo.fr> wrote:

Hello Vijaykumar,
Well, 27 e- * 0.4 = 10.8 e- which is very close to 8 (O).In addition I don't 
recognize the expected Co2+ coordination in your structure. I think evidence 
from an anomalous signal would be wellcome. Evidence from another crystal is 
not a proof for this crystal structure. It could be just a little stronger if 
the two crystals come from the same drop.
You can get anomalous info even if the crystal was not collected at the 
wavelength that maximises f". For instance, the crystal for which I provided 
the two snapshots was collected at 0.95 Angst. Not only the anomalous signal is 
well defined for the Co2+ but also for disulfide bridges. Lamdba around 1 
Angst. is a common value for native data collection on synchrotrons so that I'm 
pretty sure you can get such signal from your data.
And a good trick is to always process your data assuming the Friedel Law is not 
respected so that you can get quick access to the anomalous signal in case you 
need it.
HTH,Philippe Philippe BENAS, Ph.D.
Dog in the manger
"Un importun survient qui trouble l'intimité, qui arrête l'expansion, qui glace 
le plaisir, - probablement comme un étranger tombant au milieu d'enfants en 
train de danser une ronde", Alfred Delvau, Dictionnaire de la langue verte 
(1866).

Laboratoire de Cristallographie et RMN Biologiques, UMR 8015 CNRS
Faculté de Pharmacie, Université Paris Descartes
Case 48
Av, de l'Observatoire
F-75270 PARIS cedex 06
+33.1.5373.1599
E-mails: philippe.benas@parisdescartes. fr, philippe_be...@yahoo.fr
URLs: http://lcrbw.pharmacie.univ- paris5.fr/ , http://lcrbw.pharmacie.univ- 
paris5.fr/spip.php?article18



  De : Vijaykumar Pillalamarri <vijaypkuma...@gmail.com>
 À : CCP4BB@JISCMAIL.AC.UK 
 Envoyé le : Vendredi 27 octobre 2017 8h59
 Objet : Re: [ccp4bb] Unknown electron density
   
Dear Dr. Philippe,
There is no symmetry axis nearby the density. I did not computed anomalous map 
for this structure. In this structure, the occupancy of Co is only 0.4 (May be 
because I have added less Co).  We have proved the presence of Co in one of our 
another crystal structure of same protein.
Thanks,Vijaykumar
On 26 October 2017 at 23:11, Philippe BENAS <0d88e888355a-dmarc- 
requ...@jiscmail.ac.uk> wrote:

Dear all and Vijaykumar,
I am personally much more concerned about the Co density which does not seem as 
strong as expected for an atom with Z = 27, aren't you ?

Also I was wondering if there is no symmetry axis around your unkown density. 
Symmetry axes are often a garbage place for all the unexplained density 
everywhere else in the a.u.
Would you have by any chance computed an anomalous map ? It could help for both 
your unknown density and the Co.
Attached is a snapshot of 1.58 Angst. resolution structure showing a 2mFo-DFc 
map in blue and contoured at 2 sigma level as well as an anomalous map 
contoured at 8 sigma (snap1.png). snap2.png shows the 2mFo-DFc at 4 sigma.

Best regards,Philippe Philippe BENAS, Ph.D.
Dog in the manger
"Un importun survient qui trouble l'intimité, qui arrête l'expansion, qui glace 
le plaisir, - probablement comme un étranger tombant au milieu d'enfants en 
train de danser une ronde", Alfred Delvau, Dictionnaire de la langue verte 
(1866).

Laboratoire de Cristallographie et RMN Biologiques, UMR 8015 CNRS
Faculté de Pharmacie, Université Paris Descartes
Case 48
Av, de l'Observatoire
F-75270 PARIS cedex 06
+33.1.5373.1599
E-mails: philippe.benas@parisdescartes. fr, philippe_be...@yahoo.fr
URLs: http://lcrbw.pharmacie.univ- paris5.fr/ , http://lcrbw.pharmacie.univ- 
paris5.fr/spip.php?article18



  De : Nick Pearce <n.m.pea...@uu.nl>
 À : CCP4BB@JISCMAIL.AC.UK 
 Envoyé le : Jeudi 26 octobre 2017 18h19
 Objet : Re: [ccp4bb] Unknown electron density
  
I agree that the difference density 

Re: [ccp4bb] Unknown electron density

[Philippe BENAS]

Dear Vijaykumar,
That looks great. So now what is the distance between the Co2+ and the unknown 
density blob ? Would it be compatible with a coordination bond of the Co2+ or 
not ?

Best regards,Philippe
 Philippe BENAS, Ph.D.
Dog in the manger
"Un importun survient qui trouble l'intimité, qui arrête l'expansion, qui glace 
le plaisir, - probablement comme un étranger tombant au milieu d'enfants en 
train de danser une ronde", Alfred Delvau, Dictionnaire de la langue verte 
(1866).

Laboratoire de Cristallographie et RMN Biologiques, UMR 8015 CNRS
Faculté de Pharmacie, Université Paris Descartes
Case 48
Av, de l'Observatoire
F-75270 PARIS cedex 06
+33.1.5373.1599
E-mails: philippe.be...@parisdescartes.fr, philippe_be...@yahoo.fr
URLs: http://lcrbw.pharmacie.univ-paris5.fr/ , 
http://lcrbw.pharmacie.univ-paris5.fr/spip.php?article18



  De : Vijaykumar Pillalamarri <vijaypkuma...@gmail.com>
 À : Philippe BENAS <philippe_be...@yahoo.fr> 
Cc : "CCP4BB@JISCMAIL.AC.UK" <CCP4BB@jiscmail.ac.uk>
 Envoyé le : Vendredi 27 octobre 2017 14h08
 Objet : Re: [ccp4bb] Unknown electron density
   
Dear Philippe,
Here is the images showing anomalous map at Co contoured at 5.
Thanks,Vijaykumar
On 27 October 2017 at 14:05, Philippe BENAS <philippe_be...@yahoo.fr> wrote:

Hello Vijaykumar,
Well, 27 e- * 0.4 = 10.8 e- which is very close to 8 (O).In addition I don't 
recognize the expected Co2+ coordination in your structure. I think evidence 
from an anomalous signal would be wellcome. Evidence from another crystal is 
not a proof for this crystal structure. It could be just a little stronger if 
the two crystals come from the same drop.
You can get anomalous info even if the crystal was not collected at the 
wavelength that maximises f". For instance, the crystal for which I provided 
the two snapshots was collected at 0.95 Angst. Not only the anomalous signal is 
well defined for the Co2+ but also for disulfide bridges. Lamdba around 1 
Angst. is a common value for native data collection on synchrotrons so that I'm 
pretty sure you can get such signal from your data.
And a good trick is to always process your data assuming the Friedel Law is not 
respected so that you can get quick access to the anomalous signal in case you 
need it.
HTH,Philippe Philippe BENAS, Ph.D.
Dog in the manger
"Un importun survient qui trouble l'intimité, qui arrête l'expansion, qui glace 
le plaisir, - probablement comme un étranger tombant au milieu d'enfants en 
train de danser une ronde", Alfred Delvau, Dictionnaire de la langue verte 
(1866).

Laboratoire de Cristallographie et RMN Biologiques, UMR 8015 CNRS
Faculté de Pharmacie, Université Paris Descartes
Case 48
Av, de l'Observatoire
F-75270 PARIS cedex 06
+33.1.5373.1599
E-mails: philippe.benas@parisdescartes. fr, philippe_be...@yahoo.fr
URLs: http://lcrbw.pharmacie.univ- paris5.fr/ , http://lcrbw.pharmacie.univ- 
paris5.fr/spip.php?article18



  De : Vijaykumar Pillalamarri <vijaypkuma...@gmail.com>
 À : CCP4BB@JISCMAIL.AC.UK 
 Envoyé le : Vendredi 27 octobre 2017 8h59
 Objet : Re: [ccp4bb] Unknown electron density
   
Dear Dr. Philippe,
There is no symmetry axis nearby the density. I did not computed anomalous map 
for this structure. In this structure, the occupancy of Co is only 0.4 (May be 
because I have added less Co).  We have proved the presence of Co in one of our 
another crystal structure of same protein.
Thanks,Vijaykumar
On 26 October 2017 at 23:11, Philippe BENAS <0d88e888355a-dmarc- 
requ...@jiscmail.ac.uk> wrote:

Dear all and Vijaykumar,
I am personally much more concerned about the Co density which does not seem as 
strong as expected for an atom with Z = 27, aren't you ?

Also I was wondering if there is no symmetry axis around your unkown density. 
Symmetry axes are often a garbage place for all the unexplained density 
everywhere else in the a.u.
Would you have by any chance computed an anomalous map ? It could help for both 
your unknown density and the Co.
Attached is a snapshot of 1.58 Angst. resolution structure showing a 2mFo-DFc 
map in blue and contoured at 2 sigma level as well as an anomalous map 
contoured at 8 sigma (snap1.png). snap2.png shows the 2mFo-DFc at 4 sigma.

Best regards,Philippe Philippe BENAS, Ph.D.
Dog in the manger
"Un importun survient qui trouble l'intimité, qui arrête l'expansion, qui glace 
le plaisir, - probablement comme un étranger tombant au milieu d'enfants en 
train de danser une ronde", Alfred Delvau, Dictionnaire de la langue verte 
(1866).

Laboratoire de Cristallographie et RMN Biologiques, UMR 8015 CNRS
Faculté de Pharmacie, Université Paris Descartes
Case 48
Av, de l'Observatoire
F-75270 PARIS cedex 06
+33.1.5373.1599
E-mails: philippe.benas@parisdescartes. fr, philippe_be...@yahoo.fr
URLs: http://lcrbw.pharmacie.univ- paris5.fr/ , http://lcrbw.pharmacie.univ- 
paris5.fr/spip.php?article18



  De : Nick Pearce <n.m.pea..

Re: [ccp4bb] Unknown electron density

[Philippe BENAS]

Hello Vijaykumar,
Well, 27 e- * 0.4 = 10.8 e- which is very close to 8 (O).In addition I don't 
recognize the expected Co2+ coordination in your structure. I think evidence 
from an anomalous signal would be wellcome. Evidence from another crystal is 
not a proof for this crystal structure. It could be just a little stronger if 
the two crystals come from the same drop.
You can get anomalous info even if the crystal was not collected at the 
wavelength that maximises f". For instance, the crystal for which I provided 
the two snapshots was collected at 0.95 Angst. Not only the anomalous signal is 
well defined for the Co2+ but also for disulfide bridges. Lamdba around 1 
Angst. is a common value for native data collection on synchrotrons so that I'm 
pretty sure you can get such signal from your data.
And a good trick is to always process your data assuming the Friedel Law is not 
respected so that you can get quick access to the anomalous signal in case you 
need it.
HTH,Philippe Philippe BENAS, Ph.D.
Dog in the manger
"Un importun survient qui trouble l'intimité, qui arrête l'expansion, qui glace 
le plaisir, - probablement comme un étranger tombant au milieu d'enfants en 
train de danser une ronde", Alfred Delvau, Dictionnaire de la langue verte 
(1866).

Laboratoire de Cristallographie et RMN Biologiques, UMR 8015 CNRS
Faculté de Pharmacie, Université Paris Descartes
Case 48
Av, de l'Observatoire
F-75270 PARIS cedex 06
+33.1.5373.1599
E-mails: philippe.be...@parisdescartes.fr, philippe_be...@yahoo.fr
URLs: http://lcrbw.pharmacie.univ-paris5.fr/ , 
http://lcrbw.pharmacie.univ-paris5.fr/spip.php?article18



  De : Vijaykumar Pillalamarri <vijaypkuma...@gmail.com>
 À : CCP4BB@JISCMAIL.AC.UK 
 Envoyé le : Vendredi 27 octobre 2017 8h59
 Objet : Re: [ccp4bb] Unknown electron density
   
Dear Dr. Philippe,
There is no symmetry axis nearby the density. I did not computed anomalous map 
for this structure. In this structure, the occupancy of Co is only 0.4 (May be 
because I have added less Co).  We have proved the presence of Co in one of our 
another crystal structure of same protein.
Thanks,Vijaykumar
On 26 October 2017 at 23:11, Philippe BENAS 
<0d88e888355a-dmarc-requ...@jiscmail.ac.uk> wrote:

Dear all and Vijaykumar,
I am personally much more concerned about the Co density which does not seem as 
strong as expected for an atom with Z = 27, aren't you ?

Also I was wondering if there is no symmetry axis around your unkown density. 
Symmetry axes are often a garbage place for all the unexplained density 
everywhere else in the a.u.
Would you have by any chance computed an anomalous map ? It could help for both 
your unknown density and the Co.
Attached is a snapshot of 1.58 Angst. resolution structure showing a 2mFo-DFc 
map in blue and contoured at 2 sigma level as well as an anomalous map 
contoured at 8 sigma (snap1.png). snap2.png shows the 2mFo-DFc at 4 sigma.

Best regards,Philippe Philippe BENAS, Ph.D.
Dog in the manger
"Un importun survient qui trouble l'intimité, qui arrête l'expansion, qui glace 
le plaisir, - probablement comme un étranger tombant au milieu d'enfants en 
train de danser une ronde", Alfred Delvau, Dictionnaire de la langue verte 
(1866).

Laboratoire de Cristallographie et RMN Biologiques, UMR 8015 CNRS
Faculté de Pharmacie, Université Paris Descartes
Case 48
Av, de l'Observatoire
F-75270 PARIS cedex 06
+33.1.5373.1599
E-mails: philippe.benas@parisdescartes. fr, philippe_be...@yahoo.fr
URLs: http://lcrbw.pharmacie.univ- paris5.fr/ , http://lcrbw.pharmacie.univ- 
paris5.fr/spip.php?article18



  De : Nick Pearce <n.m.pea...@uu.nl>
 À : CCP4BB@JISCMAIL.AC.UK 
 Envoyé le : Jeudi 26 octobre 2017 18h19
 Objet : Re: [ccp4bb] Unknown electron density
  
I agree that the difference density isn’t “noise". However, just because it’s 
not noise doesn’t mean that it is modellable (with an atomic model) — the 
crystallographic density is an average over billions of molecules, and if its 
not obvious at 1.6Å what is bound, then it’s probably a superposition of states 
(or a highly disordered molecule with large B-factors, which in this case 
amounts to pretty much the same thing). When it’s a superposition of states in 
solvent regions, there are too many free parameters to build a reliable model: 
you don’t know how many alternate conformations to model, or how many species 
of molecules there are. It could be 1 conformer of PEG with 1 superposed 
conformer of water or 2 of PEG + 1 of water or 1 of PEG + 1 of something else + 
1 of water… or literally anything…
So unless you have some prior information as to what is bound, I would play it 
safe and model nothing — the conservative approach.

Thanks,Nick
—
Nick (Nicholas) PearcePost-doctoral ResearcherLab of Piet GrosCrystal & 
Structural Chemistry GroupUniversiteit Utrecht

On 26 Oct 2017, at 18:00, Vijaykumar Pillalamarri <vijaypkuma...@gmail.com> 
wr

Re: [ccp4bb] Unknown electron density

[Vijaykumar Pillalamarri]

Dear Dr. Philippe,

There is no symmetry axis nearby the density. I did not computed anomalous
map for this structure. In this structure, the occupancy of Co is only 0.4
(May be because I have added less Co).  We have proved the presence of Co
in one of our another crystal structure of same protein.

Thanks,
Vijaykumar

On 26 October 2017 at 23:11, Philippe BENAS <
0d88e888355a-dmarc-requ...@jiscmail.ac.uk> wrote:

> Dear all and Vijaykumar,
>
> I am personally much more concerned about the Co density which does not
> seem as strong as expected for an atom with Z = 27, aren't you ?
>
> Also I was wondering if there is no symmetry axis around your unkown
> density. Symmetry axes are often a garbage place for all the unexplained
> density everywhere else in the a.u.
>
> Would you have by any chance computed an anomalous map ? It could help for
> both your unknown density and the Co.
>
> Attached is a snapshot of 1.58 Angst. resolution structure showing a
> 2mFo-DFc map in blue and contoured at 2 sigma level as well as an anomalous
> map contoured at 8 sigma (snap1.png). snap2.png shows the 2mFo-DFc at 4
> sigma.
>
> Best regards,
> Philippe
>
> --
> Philippe BENAS, Ph.D.
> Dog in the manger
> "Un importun survient qui trouble l'intimité, qui arrête l'expansion, qui
> glace le plaisir, - probablement comme un étranger tombant au milieu
> d'enfants en train de danser une ronde", Alfred Delvau, Dictionnaire de
> la langue verte (1866).
>
> Laboratoire de Cristallographie et RMN Biologiques, UMR 8015 CNRS
> Faculté de Pharmacie, Université Paris Descartes
> Case 48
> <https://maps.google.com/?q=48+Av,+de+l'Observatoire=gmail=g>
> Av, de l'Observatoire
> <https://maps.google.com/?q=48+Av,+de+l'Observatoire=gmail=g>
> F-75270 PARIS cedex 06
> +33.1.5373.1599
> E-mails: philippe.be...@parisdescartes.fr, philippe_be...@yahoo.fr
> URLs: http://lcrbw.pharmacie.univ-paris5.fr/ ,
> http://lcrbw.pharmacie.univ-paris5.fr/spip.php?article18
> --
>
>
>
> --------------
> *De :* Nick Pearce <n.m.pea...@uu.nl>
> *À :* CCP4BB@JISCMAIL.AC.UK
> *Envoyé le :* Jeudi 26 octobre 2017 18h19
> *Objet :* Re: [ccp4bb] Unknown electron density
>
> I agree that the difference density isn’t “noise". However, just because
> it’s not noise doesn’t mean that it is modellable (with an atomic model) —
> the crystallographic density is an average over billions of molecules, and
> if its not obvious at 1.6Å what is bound, then it’s probably a
> superposition of states (or a highly disordered molecule with large
> B-factors, which in this case amounts to pretty much the same thing). When
> it’s a superposition of states in solvent regions, there are too many free
> parameters to build a reliable model: you don’t know how many alternate
> conformations to model, or how many species of molecules there are. It
> could be 1 conformer of PEG with 1 superposed conformer of water or 2 of
> PEG + 1 of water or 1 of PEG + 1 of something else + 1 of water… or
> literally anything…
>
> So unless you have some prior information as to what is bound, I would
> play it safe and model nothing — the conservative approach.
>
> Thanks,
> Nick
>
> —
>
> Nick (Nicholas) Pearce
> Post-doctoral Researcher
> Lab of Piet Gros
> Crystal & Structural Chemistry Group
> Universiteit Utrecht
>
> On 26 Oct 2017, at 18:00, Vijaykumar Pillalamarri <vijaypkuma...@gmail.com>
> wrote:
>
> Thanks Nick.
>
> May be it is not that weak. The blue map contour level was set to 1.5. I
> have attached another image in which the blue map is contoured to 1.0. I
> feel the green density (contoured at 3.0) is not just some noise.
>
> On 26 October 2017 at 20:38, Nick Pearce <n.m.pea...@uu.nl> wrote:
>
> Hi,
>
> Given the weakness and shapelessness of the density I doubt it is "one
> conformation of one thing", but rather a superposition of "one or more
> conformations of one or more things”. If that is the case then there
> probably isn’t enough information in the electron density or enough prior
> information to restrain a modelling approach — i.e. you could build a model
> that fit the density, but you could never determine if it was “correct”. I
> would probably just leave that bit un-modelled.
>
> Thanks,
> Nick
>
> —
>
> Nick (Nicholas) Pearce
> Post-doctoral Researcher
> Lab of Piet Gros
> Crystal & Structural Chemistry Group
> Universiteit Utrecht
>
> On 26 Oct 2017, at 16:53, Vijaykumar Pillalamarri <vijaypkuma...@gmail.com>
> wrote:
>
> Dear Dr. Vaheh,
>
&g

Re: [ccp4bb] Unknown electron density

[Nick Pearce]

I agree that the difference density isn’t “noise". However, just because it’s 
not noise doesn’t mean that it is modellable (with an atomic model) — the 
crystallographic density is an average over billions of molecules, and if its 
not obvious at 1.6Å what is bound, then it’s probably a superposition of states 
(or a highly disordered molecule with large B-factors, which in this case 
amounts to pretty much the same thing). When it’s a superposition of states in 
solvent regions, there are too many free parameters to build a reliable model: 
you don’t know how many alternate conformations to model, or how many species 
of molecules there are. It could be 1 conformer of PEG with 1 superposed 
conformer of water or 2 of PEG + 1 of water or 1 of PEG + 1 of something else + 
1 of water… or literally anything…

So unless you have some prior information as to what is bound, I would play it 
safe and model nothing — the conservative approach.

Thanks,
Nick

—

Nick (Nicholas) Pearce
Post-doctoral Researcher
Lab of Piet Gros
Crystal & Structural Chemistry Group
Universiteit Utrecht

> On 26 Oct 2017, at 18:00, Vijaykumar Pillalamarri <vijaypkuma...@gmail.com> 
> wrote:
> 
> Thanks Nick.
> 
> May be it is not that weak. The blue map contour level was set to 1.5. I have 
> attached another image in which the blue map is contoured to 1.0. I feel the 
> green density (contoured at 3.0) is not just some noise.
> 
> On 26 October 2017 at 20:38, Nick Pearce <n.m.pea...@uu.nl 
> <mailto:n.m.pea...@uu.nl>> wrote:
> Hi,
> 
> Given the weakness and shapelessness of the density I doubt it is "one 
> conformation of one thing", but rather a superposition of "one or more 
> conformations of one or more things”. If that is the case then there probably 
> isn’t enough information in the electron density or enough prior information 
> to restrain a modelling approach — i.e. you could build a model that fit the 
> density, but you could never determine if it was “correct”. I would probably 
> just leave that bit un-modelled.
> 
> Thanks,
> Nick
> 
> —
> 
> Nick (Nicholas) Pearce
> Post-doctoral Researcher
> Lab of Piet Gros
> Crystal & Structural Chemistry Group
> Universiteit Utrecht
> 
>> On 26 Oct 2017, at 16:53, Vijaykumar Pillalamarri <vijaypkuma...@gmail.com 
>> <mailto:vijaypkuma...@gmail.com>> wrote:
>> 
>> Dear Dr. Vaheh,
>> 
>> I tried fitting waters around Co but the positive density is still present 
>> even after refinement.
>> 
>> Thanks,
>> Vijaykumar
>> 
>> On 26 October 2017 at 20:19, Oganesyan, Vaheh <oganesy...@medimmune.com 
>> <mailto:oganesy...@medimmune.com>> wrote:
>> Water molecules completing Co coordination?
>> 
>>  
>> 
>> Regards,
>> 
>>  
>> 
>> Vaheh Oganesyan
>> 
>> www.medimmune.com <http://www.medimmune.com/>
>>  
>> 
>> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK 
>> <mailto:CCP4BB@JISCMAIL.AC.UK>] On Behalf Of Vijaykumar Pillalamarri
>> Sent: Thursday, October 26, 2017 10:24 AM
>> To: CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK>
>> Subject: [ccp4bb] Unknown electron density
>> 
>>  
>> 
>> Dear ccp4bb,
>> 
>>  
>> 
>> I am solving the structure of a 1.6 Angstrom data of a metallo protein. 
>> While everything else is straight forward, this density (see the picture) 
>> seems unfamiliar to me. I don't see any thing fits in the density. This 
>> density present just above Histidine-Cobalt. What ever I try to fit, the 
>> molecule clahes with histidine ( I mean the distance between His and 
>> molecule is <2 Angstrom). 
>> 
>>  
>> 
>> The crystallization condition is 0.1M Bistris, 19% PEG 3350 and 50% glycerol.
>> 
>>  
>> 
>> Any suggestions?
>> 
>>  
>> 
>> Thanks,
>> 
>> Vijaykumar Pillalamarri
>> 
>> UGC-SRF
>> 
>> C/O: Dr. Anthony Addlagatta
>> 
>> Principal Scientist
>> 
>> CSIR-IICT, Tarnaka
>> 
>> Hyderabad, India-57
>> 
>> Mobile: +918886922975
>> 
>> To the extent this electronic communication or any of its attachments 
>> contain information that is not in the public domain, such information is 
>> considered by MedImmune to be confidential and proprietary. This 
>> communication is expected to be read and/or used only by the individual(s) 
>> for whom it is intended. If you have received this electronic communication 
>> in error, please reply to the sender advising of the error in transmission 
>> and delete the original message and any accompanying documents from your 
>> system immediately, without copying, reviewing or otherwise using them for 
>> any purpose. Thank you for your cooperation.
>> 
>> 
>> 
>> -- 
>> Vijaykumar Pillalamarri
>> UGC-SRF
>> C/O: Dr. Anthony Addlagatta
>> Principal Scientist
>> CSIR-IICT, Tarnaka
>> Hyderabad, India-57
>> Mobile: +918886922975
> 
> 
> 
> 
> -- 
> Vijaykumar Pillalamarri
> UGC-SRF
> C/O: Dr. Anthony Addlagatta
> Principal Scientist
> CSIR-IICT, Tarnaka
> Hyderabad, India-57
> Mobile: +918886922975

Re: [ccp4bb] Unknown electron density

[Nick Pearce]

Hi,

Given the weakness and shapelessness of the density I doubt it is "one 
conformation of one thing", but rather a superposition of "one or more 
conformations of one or more things”. If that is the case then there probably 
isn’t enough information in the electron density or enough prior information to 
restrain a modelling approach — i.e. you could build a model that fit the 
density, but you could never determine if it was “correct”. I would probably 
just leave that bit un-modelled.

Thanks,
Nick

—

Nick (Nicholas) Pearce
Post-doctoral Researcher
Lab of Piet Gros
Crystal & Structural Chemistry Group
Universiteit Utrecht

> On 26 Oct 2017, at 16:53, Vijaykumar Pillalamarri <vijaypkuma...@gmail.com> 
> wrote:
> 
> Dear Dr. Vaheh,
> 
> I tried fitting waters around Co but the positive density is still present 
> even after refinement.
> 
> Thanks,
> Vijaykumar
> 
> On 26 October 2017 at 20:19, Oganesyan, Vaheh <oganesy...@medimmune.com 
> <mailto:oganesy...@medimmune.com>> wrote:
> Water molecules completing Co coordination?
> 
>  
> 
> Regards,
> 
>  
> 
> Vaheh Oganesyan
> 
> www.medimmune.com <http://www.medimmune.com/>
>  
> 
> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK 
> <mailto:CCP4BB@JISCMAIL.AC.UK>] On Behalf Of Vijaykumar Pillalamarri
> Sent: Thursday, October 26, 2017 10:24 AM
> To: CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK>
> Subject: [ccp4bb] Unknown electron density
> 
>  
> 
> Dear ccp4bb,
> 
>  
> 
> I am solving the structure of a 1.6 Angstrom data of a metallo protein. While 
> everything else is straight forward, this density (see the picture) seems 
> unfamiliar to me. I don't see any thing fits in the density. This density 
> present just above Histidine-Cobalt. What ever I try to fit, the molecule 
> clahes with histidine ( I mean the distance between His and molecule is <2 
> Angstrom). 
> 
>  
> 
> The crystallization condition is 0.1M Bistris, 19% PEG 3350 and 50% glycerol.
> 
>  
> 
> Any suggestions?
> 
>  
> 
> Thanks,
> 
> Vijaykumar Pillalamarri
> 
> UGC-SRF
> 
> C/O: Dr. Anthony Addlagatta
> 
> Principal Scientist
> 
> CSIR-IICT, Tarnaka
> 
> Hyderabad, India-57
> 
> Mobile: +918886922975
> 
> To the extent this electronic communication or any of its attachments contain 
> information that is not in the public domain, such information is considered 
> by MedImmune to be confidential and proprietary. This communication is 
> expected to be read and/or used only by the individual(s) for whom it is 
> intended. If you have received this electronic communication in error, please 
> reply to the sender advising of the error in transmission and delete the 
> original message and any accompanying documents from your system immediately, 
> without copying, reviewing or otherwise using them for any purpose. Thank you 
> for your cooperation.
> 
> 
> 
> -- 
> Vijaykumar Pillalamarri
> UGC-SRF
> C/O: Dr. Anthony Addlagatta
> Principal Scientist
> CSIR-IICT, Tarnaka
> Hyderabad, India-57
> Mobile: +918886922975

Re: [ccp4bb] Unknown electron density

[Parthasarathy Sampathkumar]

Hi Vijay,

Why there is no 2mFo-DFc (blue) feature on this mFo-DFc (green) map?!! Is
the contour level for blue map set high?!! If there is no 2mFo-DFc density,
should this be consider as noise?!!

Hope this helps,
Best Wishes,
Partha


On Thu, Oct 26, 2017 at 10:23 AM, Vijaykumar Pillalamarri <
vijaypkuma...@gmail.com> wrote:

> Dear ccp4bb,
>
> I am solving the structure of a 1.6 Angstrom data of a metallo protein.
> While everything else is straight forward, this density (see the picture)
> seems unfamiliar to me. I don't see any thing fits in the density. This
> density present just above Histidine-Cobalt. What ever I try to fit, the
> molecule clahes with histidine ( I mean the distance between His and
> molecule is <2 Angstrom).
>
> The crystallization condition is 0.1M Bistris, 19% PEG 3350 and 50%
> glycerol.
>
> Any suggestions?
>
> Thanks,
> Vijaykumar Pillalamarri
> UGC-SRF
> C/O: Dr. Anthony Addlagatta
> Principal Scientist
> CSIR-IICT, Tarnaka
> Hyderabad, India-57
> Mobile: +918886922975 <+91%2088869%2022975>
>

Re: [ccp4bb] Unknown electron density

[Vijaykumar Pillalamarri]

Dear Dr. Vaheh,

I tried fitting waters around Co but the positive density is still present
even after refinement.

Thanks,
Vijaykumar

On 26 October 2017 at 20:19, Oganesyan, Vaheh <oganesy...@medimmune.com>
wrote:

> Water molecules completing Co coordination?
>
>
>
> *Regards,*
>
>
>
> *Vaheh Oganesyan*
>
> *www.medimmune.com <http://www.medimmune.com>*
>
>
>
> *From:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *On Behalf Of 
> *Vijaykumar
> Pillalamarri
> *Sent:* Thursday, October 26, 2017 10:24 AM
> *To:* CCP4BB@JISCMAIL.AC.UK
> *Subject:* [ccp4bb] Unknown electron density
>
>
>
> Dear ccp4bb,
>
>
>
> I am solving the structure of a 1.6 Angstrom data of a metallo protein.
> While everything else is straight forward, this density (see the picture)
> seems unfamiliar to me. I don't see any thing fits in the density. This
> density present just above Histidine-Cobalt. What ever I try to fit, the
> molecule clahes with histidine ( I mean the distance between His and
> molecule is <2 Angstrom).
>
>
>
> The crystallization condition is 0.1M Bistris, 19% PEG 3350 and 50%
> glycerol.
>
>
>
> Any suggestions?
>
>
>
> Thanks,
>
> Vijaykumar Pillalamarri
>
> UGC-SRF
>
> C/O: Dr. Anthony Addlagatta
>
> Principal Scientist
>
> CSIR-IICT, Tarnaka
>
> Hyderabad, India-57
>
> Mobile: +918886922975
> To the extent this electronic communication or any of its attachments
> contain information that is not in the public domain, such information is
> considered by MedImmune to be confidential and proprietary. This
> communication is expected to be read and/or used only by the individual(s)
> for whom it is intended. If you have received this electronic communication
> in error, please reply to the sender advising of the error in transmission
> and delete the original message and any accompanying documents from your
> system immediately, without copying, reviewing or otherwise using them for
> any purpose. Thank you for your cooperation.
>



-- 
Vijaykumar Pillalamarri
UGC-SRF
C/O: Dr. Anthony Addlagatta
Principal Scientist
CSIR-IICT, Tarnaka
Hyderabad, India-57
Mobile: +918886922975

Re: [ccp4bb] Unknown electron density blob, pdb convention for partially ordered ligands

[Robbie Joosten]

Hi Tristan,



There are PDB entries that have this, but this makes matters a bit more 
complicated in annotation. You have to define LINKs and leaving atoms. 
Consistency would be nice here, but that is lacking in these entries.



Cheers,

Robbie



Sent from my Windows 10 phone



Van: Tristan Croll<mailto:ti...@cam.ac.uk>
Verzonden: woensdag 25 januari 2017 18:30
Aan: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>
Onderwerp: Re: [ccp4bb] Unknown electron density blob, pdb convention for 
partially ordered ligands



I've often wondered about PEG (and, I guess, other synthetic polymers): 
wouldn't it just be better to define the monomer, and then model a chain of 
however many monomers you need?

T



Tristan Croll
Research Fellow
Cambridge Institute for Medical Research
University of Cambridge CB2 0XY




> On 25 Jan 2017, at 17:21, Edward A. Berry <ber...@upstate.edu> wrote:
>
> Uma's use of quotes around "di" suggests a related question about PDB 
> convention. It was my (perhaps not very good) understanding that ligands 
> should be identified by what is actually present in the crystal, and not by 
> what can be modeled. For example endogenous ubiquinone is likely to be UQ50 
> (depending on the species) but most of that 50-carbon side chain is hanging 
> out in the lipid or detergent and completely disordered. Still we should use 
> the ligand identifier for UQ50, even though codes exist for UQ with 5 or 
> 10-carbon side chains that are much better accommodated by the density.
>
> If that is the case, one should not use the pdb identifier for diethylene 
> glycol (PEG) when PEG4k was the precipitant, unless you believe that the 
> binding site has specifically selected diethylene glycol from an extremely 
> broad range of polymer lengths in the added material.  Using the identifier 
> for a much longer PEG will result in a large number of "missing atoms" listed 
> in the report, but would eliminate the unreasonable assumption that PEG 
> fragment models must always end with a terminal oxygen.
>
> Even if that is the rule, I would agree that PEGs would be a good place to 
> ignore the rule. Since PEGs have a MW distribution, it is impossible to know 
> exactly what is bound and it may be different in different unit cells. If you 
> are not going to get it right no matter what you put, you might as well put 
> something that fits.
> eab
>
>> On 01/25/2017 09:51 AM, Uma Gabale wrote:
>> Dear all,
>> Thank you very much for your replies. It is a PEG, a "di"ethylene glycol to 
>> be precise, in most chains.
>> Best regards,
>> Uma.
>> --
>> Uma Gabale, PhD
>> Research Associate
>> Molecular and Cellular Biochemistry
>> Indiana University Bloomington
>>

Re: [ccp4bb] Unknown electron density blob, pdb convention for partially ordered ligands

[Tristan Croll]

I've often wondered about PEG (and, I guess, other synthetic polymers): 
wouldn't it just be better to define the monomer, and then model a chain of 
however many monomers you need?

T

 
 
Tristan Croll
Research Fellow
Cambridge Institute for Medical Research
University of Cambridge CB2 0XY
 

 

> On 25 Jan 2017, at 17:21, Edward A. Berry  wrote:
> 
> Uma's use of quotes around "di" suggests a related question about PDB 
> convention. It was my (perhaps not very good) understanding that ligands 
> should be identified by what is actually present in the crystal, and not by 
> what can be modeled. For example endogenous ubiquinone is likely to be UQ50 
> (depending on the species) but most of that 50-carbon side chain is hanging 
> out in the lipid or detergent and completely disordered. Still we should use 
> the ligand identifier for UQ50, even though codes exist for UQ with 5 or 
> 10-carbon side chains that are much better accommodated by the density.
> 
> If that is the case, one should not use the pdb identifier for diethylene 
> glycol (PEG) when PEG4k was the precipitant, unless you believe that the 
> binding site has specifically selected diethylene glycol from an extremely 
> broad range of polymer lengths in the added material.  Using the identifier 
> for a much longer PEG will result in a large number of "missing atoms" listed 
> in the report, but would eliminate the unreasonable assumption that PEG 
> fragment models must always end with a terminal oxygen.
> 
> Even if that is the rule, I would agree that PEGs would be a good place to 
> ignore the rule. Since PEGs have a MW distribution, it is impossible to know 
> exactly what is bound and it may be different in different unit cells. If you 
> are not going to get it right no matter what you put, you might as well put 
> something that fits.
> eab
> 
>> On 01/25/2017 09:51 AM, Uma Gabale wrote:
>> Dear all,
>> Thank you very much for your replies. It is a PEG, a "di"ethylene glycol to 
>> be precise, in most chains.
>> Best regards,
>> Uma.
>> --
>> Uma Gabale, PhD
>> Research Associate
>> Molecular and Cellular Biochemistry
>> Indiana University Bloomington
>> 

Re: [ccp4bb] Unknown electron density blob, pdb convention for partially ordered ligands

[Edward A. Berry]

Uma's use of quotes around "di" suggests a related question about PDB 
convention. It was my (perhaps not very good) understanding that ligands should be 
identified by what is actually present in the crystal, and not by what can be modeled. 
For example endogenous ubiquinone is likely to be UQ50 (depending on the species) but 
most of that 50-carbon side chain is hanging out in the lipid or detergent and completely 
disordered. Still we should use the ligand identifier for UQ50, even though codes exist 
for UQ with 5 or 10-carbon side chains that are much better accommodated by the density.

If that is the case, one should not use the pdb identifier for diethylene glycol (PEG) 
when PEG4k was the precipitant, unless you believe that the binding site has specifically 
selected diethylene glycol from an extremely broad range of polymer lengths in the added 
material.  Using the identifier for a much longer PEG will result in a large number of 
"missing atoms" listed in the report, but would eliminate the unreasonable 
assumption that PEG fragment models must always end with a terminal oxygen.

Even if that is the rule, I would agree that PEGs would be a good place to 
ignore the rule. Since PEGs have a MW distribution, it is impossible to know 
exactly what is bound and it may be different in different unit cells. If you 
are not going to get it right no matter what you put, you might as well put 
something that fits.
eab

On 01/25/2017 09:51 AM, Uma Gabale wrote:

Dear all,
Thank you very much for your replies. It is a PEG, a "di"ethylene glycol to be 
precise, in most chains.
Best regards,
Uma.
--
Uma Gabale, PhD
Research Associate
Molecular and Cellular Biochemistry
Indiana University Bloomington

Re: [ccp4bb] Unknown electron density blob

[Uma Gabale]

Dear all,Thank you very much for your replies. It is a PEG, a "di"ethylene 
glycol to be precise, in most chains. Best regards,Uma. --Uma Gabale, 
PhDResearch AssociateMolecular and Cellular Biochemistry
Indiana University Bloomington
 
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Re: [ccp4bb] Unknown electron density blob

[Robbie Joosten]

PEG likes to hang around where it is unwelcome: 
http://onlinelibrary.wiley.com/doi/10.1002/pro.2923/full

Cheers,
Robbie

Sent from my Windows 10 phone

Van: Bernhard Rupp<mailto:hofkristall...@gmail.com>
Verzonden: dinsdag 24 januari 2017 23:20
Aan: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>
Onderwerp: Re: [ccp4bb] Unknown electron density blob

Some general remarks about PEG modelling and associated caveats:
http://journals.iucr.org/d/issues/2016/12/00/rr5136/index.html
Section 3.6.5.

Best, BR

From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Ana Luísa 
Moreira de Carvalho
Sent: Tuesday, January 24, 2017 10:11 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Unknown electron density blob

Just to add to this, in our group, we had a funny case where we found PEG 
around K:

https://drive.google.com/open?id=0B2DrnhrLgvwGSldLVl9pSEptakE
https://drive.google.com/open?id=0B2DrnhrLgvwGZlNiYTFoaktPUHc

Ana Luisa


On 24 Jan 2017, at 17:36, Artem Evdokimov 
<artem.evdoki...@gmail.com<mailto:artem.evdoki...@gmail.com>> wrote:

PEG. It wraps around K or R residues just like you are showing.

Artem
www.harkerbio.com<http://www.harkerbio.com/>
"where every blob has candy inside"

On Jan 24, 2017 12:19 PM, "Uma Gabale" 
<0ebb5dcf3eaa-dmarc-requ...@jiscmail.ac.uk<mailto:0ebb5dcf3eaa-dmarc-requ...@jiscmail.ac.uk>>
 wrote:
Dear all,
While refining a structure at 2.5 A resolution, we observed a 
semi-circular/crescent shaped electron density blob as shown in the attached 
picture. We have been unable to identify it so far, and would appreciate any 
help in identification.
The protein was expressed in E. coli BL21(DE3), purified on Ni-NTA followed by 
gel filtration. The purification buffers included Tris and NaCl (no detergent/ 
other ingredients except for imidazole for Ni-NTA). Crystallization condition 
had HEPES and PEG3350; no cryoprotectant was used.
The blob is surrounded by residues Trp, Thr, Gln, Arg, and Phe.
Thanks and regards,
Uma.

--
Uma Gabale, PhD
Research Associate
Molecular and Cellular Biochemistry
Indiana University Bloomington

Research Assistant Professor at UCIBIO@REQUIMTE-FCT-NOVA
***
Biologia Estrutural - Cristalografia de Raios-X (Gab 6.34)
Dep. Quimica, FCT-UNL
2829-516 Caparica
Portugal
Phone: 00351212948300 (ext: Gab: 10940; Lab: 10962; X-ray Lab: 10915)
Fax: 00351212948550
http://docentes.fct.unl.pt/almc
http://sites.fct.unl.pt/xtal
https://www.facebook.com/XtalNOVA/
***
Single Crystal X-ray Structure Determination Service: 
http://www.dq.fct.unl.pt/en/single-crystal-x-ray-structure-determination

Re: [ccp4bb] Unknown electron density blob

[Bernhard Rupp]

Some general remarks about PEG modelling and associated caveats:

http://journals.iucr.org/d/issues/2016/12/00/rr5136/index.html

Section 3.6.5.

 

Best, BR

 

From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Ana
Luísa Moreira de Carvalho
Sent: Tuesday, January 24, 2017 10:11 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Unknown electron density blob

 

Just to add to this, in our group, we had a funny case where we found PEG
around K:

 

https://drive.google.com/open?id=0B2DrnhrLgvwGSldLVl9pSEptakE

https://drive.google.com/open?id=0B2DrnhrLgvwGZlNiYTFoaktPUHc

 

Ana Luisa

 

 

On 24 Jan 2017, at 17:36, Artem Evdokimov <artem.evdoki...@gmail.com
<mailto:artem.evdoki...@gmail.com> > wrote:

 

PEG. It wraps around K or R residues just like you are showing.

 

Artem

www.harkerbio.com <http://www.harkerbio.com/> 

"where every blob has candy inside"

 

On Jan 24, 2017 12:19 PM, "Uma Gabale"
<0ebb5dcf3eaa-dmarc-requ...@jiscmail.ac.uk
<mailto:0ebb5dcf3eaa-dmarc-requ...@jiscmail.ac.uk> > wrote:

Dear all,

While refining a structure at 2.5 A resolution, we observed a
semi-circular/crescent shaped electron density blob as shown in the attached
picture. We have been unable to identify it so far, and would appreciate any
help in identification.

The protein was expressed in E. coli BL21(DE3), purified on Ni-NTA followed
by gel filtration. The purification buffers included Tris and NaCl (no
detergent/ other ingredients except for imidazole for Ni-NTA).
Crystallization condition had HEPES and PEG3350; no cryoprotectant was used.

The blob is surrounded by residues Trp, Thr, Gln, Arg, and Phe.

Thanks and regards,

Uma.

 

--

Uma Gabale, PhD

Research Associate

Molecular and Cellular Biochemistry
Indiana University Bloomington

 

Research Assistant Professor at UCIBIO@REQUIMTE-FCT-NOVA

***
Biologia Estrutural - Cristalografia de Raios-X (Gab 6.34)
Dep. Quimica, FCT-UNL
2829-516 Caparica
Portugal
Phone: 00351212948300 (ext: Gab: 10940; Lab: 10962; X-ray Lab: 10915)
Fax: 00351212948550
 <http://docentes.fct.unl.pt/almc> http://docentes.fct.unl.pt/almc
http://sites.fct.unl.pt/xtal

https://www.facebook.com/XtalNOVA/
***

Single Crystal X-ray Structure Determination Service:
http://www.dq.fct.unl.pt/en/single-crystal-x-ray-structure-determination

 

Re: [ccp4bb] Unknown electron density blob

[Ana Luísa Moreira de Carvalho]

Just to add to this, in our group, we had a funny case where we found PEG 
around K:

https://drive.google.com/open?id=0B2DrnhrLgvwGSldLVl9pSEptakE
https://drive.google.com/open?id=0B2DrnhrLgvwGZlNiYTFoaktPUHc

Ana Luisa


> On 24 Jan 2017, at 17:36, Artem Evdokimov  wrote:
> 
> PEG. It wraps around K or R residues just like you are showing.
> 
> Artem
> www.harkerbio.com 
> "where every blob has candy inside"
> 
> On Jan 24, 2017 12:19 PM, "Uma Gabale" 
> <0ebb5dcf3eaa-dmarc-requ...@jiscmail.ac.uk 
> > wrote:
> Dear all,
> While refining a structure at 2.5 A resolution, we observed a 
> semi-circular/crescent shaped electron density blob as shown in the attached 
> picture. We have been unable to identify it so far, and would appreciate any 
> help in identification.
> The protein was expressed in E. coli BL21(DE3), purified on Ni-NTA followed 
> by gel filtration. The purification buffers included Tris and NaCl (no 
> detergent/ other ingredients except for imidazole for Ni-NTA). 
> Crystallization condition had HEPES and PEG3350; no cryoprotectant was used.
> The blob is surrounded by residues Trp, Thr, Gln, Arg, and Phe.
> Thanks and regards,
> Uma.
> 
> --
> Uma Gabale, PhD
> Research Associate
> Molecular and Cellular Biochemistry
> Indiana University Bloomington

Research Assistant Professor at UCIBIO@REQUIMTE-FCT-NOVA
***
Biologia Estrutural - Cristalografia de Raios-X (Gab 6.34)
Dep. Quimica, FCT-UNL
2829-516 Caparica
Portugal
Phone: 00351212948300 (ext: Gab: 10940; Lab: 10962; X-ray Lab: 10915)
Fax: 00351212948550
http://docentes.fct.unl.pt/almc 
http://sites.fct.unl.pt/xtal
https://www.facebook.com/XtalNOVA/
***
Single Crystal X-ray Structure Determination Service: 
http://www.dq.fct.unl.pt/en/single-crystal-x-ray-structure-determination

Re: [ccp4bb] Unknown electron density blob

[Vivoli, Mirella]

Hi there,

I think it is PEG, very common to have PEG in horseshoe shape with arginine 
pointing toward to it.

Cheers,


Mirella


Vivoli Mirella

Associate Research Fellow
Biocatalysis Centre, Henry Wellcome Building
College of Life and Environmental Sciences,
University of Exeter
Stocker Road
Exeter
Ex4 4QD
Tel: + 44 (0)1392 726121
Email: m.viv...@exeter.ac.uk

"I don't want to believe. I want to know". [C. Sagan]

From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Paul Emsley 
<pems...@mrc-lmb.cam.ac.uk>
Sent: 24 January 2017 17:32:35
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Unknown electron density blob

On 24/01/2017 17:19, Uma Gabale wrote:

> While refining a structure at 2.5 A resolution, we observed a 
> semi-circular/crescent shaped
> electron density blob as shown in the attached picture. We have been unable 
> to identify it
> so far, and would appreciate any help in identification.

If you have Coot:

Extensions->Modelling->Add Other Solvent Molecules->Add New Residue 
Type->"PG4"->Add
then click "PG4 Tetraethylene Glycol"

Re: [ccp4bb] Unknown electron density blob

[Artem Evdokimov]

PEG. It wraps around K or R residues just like you are showing.

Artem
www.harkerbio.com
"where every blob has candy inside"

On Jan 24, 2017 12:19 PM, "Uma Gabale" <
0ebb5dcf3eaa-dmarc-requ...@jiscmail.ac.uk> wrote:

> Dear all,
> While refining a structure at 2.5 A resolution, we observed a
> semi-circular/crescent shaped electron density blob as shown in the
> attached picture. We have been unable to identify it so far, and would
> appreciate any help in identification.
> The protein was expressed in *E. coli* BL21(DE3), purified on Ni-NTA
> followed by gel filtration. The purification buffers included Tris and NaCl
> (no detergent/ other ingredients except for imidazole for Ni-NTA).
> Crystallization condition had HEPES and PEG3350; no cryoprotectant was used.
> The blob is surrounded by residues Trp, Thr, Gln, Arg, and Phe.
> Thanks and regards,
> Uma.
>
> --
> Uma Gabale, PhD
> Research Associate
> Molecular and Cellular Biochemistry
> Indiana University Bloomington
>

Re: [ccp4bb] Unknown electron density blob

[Parthasarathy Sampathkumar]

Hi Uma,

It is risky to guess based on one-view of of the density from 2-dimensional
images. What is the contour-level of 2mFo-DFc (blue) map displayed here?!!
If 2mFo-DFc density is continuous from Arg, say at 0.8 sigma, then could it
be an alternate conformation of the Arg side-chain. One could build, and
re-refine and see if negative mFo-DFc features shows up.

Hope this helps,
Partha

On Tue, Jan 24, 2017 at 12:19 PM, Uma Gabale <
0ebb5dcf3eaa-dmarc-requ...@jiscmail.ac.uk> wrote:

> Dear all,
> While refining a structure at 2.5 A resolution, we observed a
> semi-circular/crescent shaped electron density blob as shown in the
> attached picture. We have been unable to identify it so far, and would
> appreciate any help in identification.
> The protein was expressed in *E. coli* BL21(DE3), purified on Ni-NTA
> followed by gel filtration. The purification buffers included Tris and NaCl
> (no detergent/ other ingredients except for imidazole for Ni-NTA).
> Crystallization condition had HEPES and PEG3350; no cryoprotectant was used.
> The blob is surrounded by residues Trp, Thr, Gln, Arg, and Phe.
> Thanks and regards,
> Uma.
>
> --
> Uma Gabale, PhD
> Research Associate
> Molecular and Cellular Biochemistry
> Indiana University Bloomington
>

Re: [ccp4bb] Unknown electron density blob

[Paul Emsley]

On 24/01/2017 17:32, Paul Emsley wrote:

On 24/01/2017 17:19, Uma Gabale wrote:


While refining a structure at 2.5 A resolution, we observed a 
semi-circular/crescent shaped
electron density blob as shown in the attached picture. We have been unable to 
identify it
so far, and would appreciate any help in identification.


If you have Coot:

Extensions->Modelling->Add Other Solvent Molecules->Add New Residue 
Type->"PG4"->Add
then click "PG4 Tetraethylene Glycol"


Delete the water first, obviously.

Re: [ccp4bb] Unknown electron density blob

[Paul Emsley]

On 24/01/2017 17:19, Uma Gabale wrote:


While refining a structure at 2.5 A resolution, we observed a 
semi-circular/crescent shaped
electron density blob as shown in the attached picture. We have been unable to 
identify it
so far, and would appreciate any help in identification.


If you have Coot:

Extensions->Modelling->Add Other Solvent Molecules->Add New Residue 
Type->"PG4"->Add
then click "PG4 Tetraethylene Glycol"

Re: [ccp4bb] Unknown electron density blob

[Boaz Shaanan]

Hi,


Could it be a segment of peg3350?


  Cheers,


              Boaz


 
 
Boaz Shaanan, Ph.D.

Dept. of Life Sciences  
Ben-Gurion University of the Negev  
Beer-Sheva 84105    
Israel  
    
E-mail: bshaa...@bgu.ac.il
Phone: 972-8-647-2220  Skype: boaz.shaanan  
Fax:   972-8-647-2992 or 972-8-646-1710
 
 








From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Uma Gabale [0ebb5dcf3eaa-dmarc-requ...@jiscmail.ac.uk]
Sent: Tuesday, January 24, 2017 7:19 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Unknown electron density blob





Dear all,
While refining a structure at 2.5 A resolution, we observed a semi-circular/crescent shaped electron density blob as shown in the attached picture. We have been unable to identify it so far, and would
 appreciate any help in identification.
The protein was expressed in
E. coli BL21(DE3), purified on Ni-NTA followed by gel filtration. The purification buffers included Tris and NaCl (no detergent/ other ingredients except for imidazole for Ni-NTA). Crystallization condition
 had HEPES and PEG3350; no cryoprotectant was used.
The blob is surrounded by residues Trp,
Thr,
Gln,
Arg, and Phe.
Thanks and regards,
Uma.



--
Uma Gabale, PhD

Research Associate

Molecular and Cellular Biochemistry
Indiana University Bloomington

Re: [ccp4bb] unknown electron density~

[Artem Evdokimov]

Try fitting a xylitol molecule in it but watch out for the distortions
caused by proximity to symmetry axis.

Artem

On Thu, Mar 31, 2011 at 1:16 PM, Shu XU xushuh...@gmail.com wrote:

 Hi, there.
 I'm refining a 1.76 A structure. The r-work stuck at 21%, rfree is 24%
 after adding waters.
 But there is something between the interfaces of the dimers.
 The space group is I4122, so it looks like something small, five or
 six atoms all together (without hydrogens).
 I tried to fit Tris in, however, it didn't look good at all.
 The crystal came out from Tris-cl buffer, ammonium sulfate, and there
 is some NaCl in the protein buffer too.
 The crystals were dropped into 20% xylitol and flash frozen.
 Fo-Fc maps are attached at 3 sigma level.
 Let me know what you're thoughts are.
 Thank you for your help.

 Shu


 --
 Shu Xu
 Ph.D candidate in Chemistry
 Department of Chemistry
 The University of Toledo
 Toledo, OH 43606
 Tel 419-530-1524