Re: [ccp4bb] Unknown positive electron density

[Eleanor Dodson]

I am even more cautious - if I want to check the anomalous map for a strong
scatterer  I set the putative anomalous scatterer occupancy to 0.0 .
 Theoretically it shouldn't be necessary - the atom map uses Phic+90 (or
maybe Phic -90??) but if the site is excluded you feel more secure in
drawing conclusions.

Eleanor

On 25 August 2017 at 20:31, James Holton  wrote:

> That just looks like bulk solvent to me.  Might be extra dense to the the
> barium, but disordered bulk nonetheless.
>
> If, as you say, the anomalous peak only shows up after you model in a
> strong anomalous scatterrer and not when you don't model in anomalous
> signal, then I suspect all you are seeing is the fabled "model bias".  Weak
> signals (like anomalous) are particularly sensitive to this.
>
> It is an interesting test to try:
> 1) measure the anomalous difference peak height after refinement (I use
> "peakmax" in CCP4)
> 2) set the Ba atom's f" value to 0, and re-refine to convergence.  What is
> the peak value now?
> 3) set the Ba atom's f" value to twice what you expect theoretically.
> Re-refine. Now what do you see?
>
> Once you've done this, you should have a good feeling for how much of your
> anomalous peak is coming from your model vs from your data.
>
> -James Holton
> MAD Scientist
>
>
> On 8/21/2017 3:05 PM, Betty Chu wrote:
>
> Hi Craig,
>
> The data collection wavelength was 0.92 Angstroms. Since we observe
> anomalous signal for Ba at this wavelength, we would expect greater
> anomalous signal if As were present. There is a possibility for weak
> anomalous signal in this positive density, but the weak anomalous signal
> only shows up if I try to model a Ba in the density. Without modelling
> anything, there is no anomalous signal.
>
> This is what the map looks like after one round of refinement with the Ba
> in the density. But since there are waters that are 1.6 Angstroms, 1.9
> Angstroms, and 2.2 Angstroms away from the Ba, which is smaller than the
> coordination distance between Ba and water, we are skeptical of the Ba
> being there.
>
> https://cbsostorage.chem.umd.edu/owncloud/index.php/s/O4lI2iKvRsQUoRo
>
> Thank you,
> Betty
>
> On Mon, Aug 21, 2017 at 5:21 PM, CRAIG A BINGMAN 
> wrote:
>
>> What is the data collection wavelength/energy? Would you expect
>> significant anomalous diffraction from As at this wavelength?
>>
>> On Aug 21, 2017, at 11:37 AM, Betty Chu  wrote:
>>
>> Hi Shailesh,
>>
>> When I modelled in the Barium ion with octahedrally coordinated waters
>> and ran the refinement, the distances from the barium to some of the waters
>> ended up being too close (<2.2 Angstroms). Also, the positive electron
>> density is connected. If the density indicated barium with coordinated
>> waters, would that mean there are multiple ones present in the positive
>> density?
>>
>> Here are more views of the connected positive density.
>>
>> https://cbsostorage.chem.umd.edu/owncloud/index.php/s/j5CgZIJe6NKgUlZ
>>
>> https://cbsostorage.chem.umd.edu/owncloud/index.php/s/YbiNFbT8AW1iHUQ
>>
>> On Mon, Aug 21, 2017 at 12:00 PM, Shailesh Tripathi > > wrote:
>>
>>> Looks like Ba2+. Since it exist with coordination number 6 or above
>>> check what geometry water is following there (trigonal bipiramidal or so
>>> on). Water might also be shared by symmetry related Ba cation.
>>>
>>>
>>>
>>> Shailesh Kumar Tripathi,
>>> Phone: 9686289668
>>>
>>>
>>> On Mon, Aug 21, 2017 at 9:17 PM, Betty Chu  wrote:
>>>
 Yes, I have. The cacodylate ion does not fit well into the density.

 On Mon, Aug 21, 2017 at 11:44 AM, Pradeep Pallan <
 pradeeppal...@gmail.com> wrote:

> Did you try modelling in a cacodylate ion (CH3)2AsO2-?
>
> On Mon, Aug 21, 2017 at 10:19 AM, Betty Chu  wrote:
>
>> Dear ccp4bb,
>>
>> I am refining a 1.40 Angstrom data set for a DNA oligonucleotide.
>> While the model for the DNA fits very well into the density, there is a
>> patch of positive electron density in the solvent space that we are 
>> having
>> trouble with.
>>
>> The screenshot can be viewed through this link:
>> https://cbsostorage.chem.umd.edu/owncloud/index.php/s/J5cKnOpCC4vb1VC
>>
>> In the screenshot, the yellow color is the anomalous map and a barium
>> ion is fitted into density near the positive green electron density.
>>
>> The oligonucleotide was purchased from IDT. The crystallization
>> condition is 15% MPD, 120 mM BaCl2, and 30 mM NaCaC pH 6.4. I have tried
>> modelling Ba2+ with coordinated waters, MPD, and sodium cacodylate into 
>> the
>> electron density, but none of those fit well.
>>
>> Any suggestions regarding the identity of this electron density is
>> much appreciated. Thank you!
>>
>> Sincerely,
>>
>> Betty Chu
>> Paukstelis Research Group
>> Department of 

Re: [ccp4bb] Unknown positive electron density

[James Holton]

That just looks like bulk solvent to me.  Might be extra dense to the 
the barium, but disordered bulk nonetheless.


If, as you say, the anomalous peak only shows up after you model in a 
strong anomalous scatterrer and not when you don't model in anomalous 
signal, then I suspect all you are seeing is the fabled "model bias".  
Weak signals (like anomalous) are particularly sensitive to this.


It is an interesting test to try:
1) measure the anomalous difference peak height after refinement (I use 
"peakmax" in CCP4)
2) set the Ba atom's f" value to 0, and re-refine to convergence. What 
is the peak value now?
3) set the Ba atom's f" value to twice what you expect theoretically.  
Re-refine. Now what do you see?


Once you've done this, you should have a good feeling for how much of 
your anomalous peak is coming from your model vs from your data.


-James Holton
MAD Scientist

On 8/21/2017 3:05 PM, Betty Chu wrote:

Hi Craig,

The data collection wavelength was 0.92 Angstroms. Since we observe 
anomalous signal for Ba at this wavelength, we would expect greater 
anomalous signal if As were present. There is a possibility for weak 
anomalous signal in this positive density, but the weak anomalous 
signal only shows up if I try to model a Ba in the density. Without 
modelling anything, there is no anomalous signal.


This is what the map looks like after one round of refinement with the 
Ba in the density. But since there are waters that are 1.6 Angstroms, 
1.9 Angstroms, and 2.2 Angstroms away from the Ba, which is smaller 
than the coordination distance between Ba and water, we are skeptical 
of the Ba being there.


https://cbsostorage.chem.umd.edu/owncloud/index.php/s/O4lI2iKvRsQUoRo 



Thank you,
Betty

On Mon, Aug 21, 2017 at 5:21 PM, CRAIG A BINGMAN > wrote:


What is the data collection wavelength/energy? Would you expect
significant anomalous diffraction from As at this wavelength?


On Aug 21, 2017, at 11:37 AM, Betty Chu > wrote:

Hi Shailesh,

When I modelled in the Barium ion with octahedrally coordinated
waters and ran the refinement, the distances from the barium to
some of the waters ended up being too close (<2.2 Angstroms).
Also, the positive electron density is connected. If the density
indicated barium with coordinated waters, would that mean there
are multiple ones present in the positive density?

Here are more views of the connected positive density.

https://cbsostorage.chem.umd.edu/owncloud/index.php/s/j5CgZIJe6NKgUlZ


https://cbsostorage.chem.umd.edu/owncloud/index.php/s/YbiNFbT8AW1iHUQ


On Mon, Aug 21, 2017 at 12:00 PM, Shailesh Tripathi
> wrote:

Looks like Ba2+. Since it exist with coordination number 6 or
above check what geometry water is following there (trigonal
bipiramidal or so on). Water might also be shared by symmetry
related Ba cation.



Shailesh Kumar Tripathi,
Phone: 9686289668


On Mon, Aug 21, 2017 at 9:17 PM, Betty Chu > wrote:

Yes, I have. The cacodylate ion does not fit well into
the density.

On Mon, Aug 21, 2017 at 11:44 AM, Pradeep Pallan
> wrote:

Did you try modelling in a cacodylate ion (CH3)2AsO2-?

On Mon, Aug 21, 2017 at 10:19 AM, Betty Chu
> wrote:

Dear ccp4bb,

I am refining a 1.40 Angstrom data set for a DNA
oligonucleotide. While the model for the DNA fits
very well into the density, there is a patch of
positive electron density in the solvent space
that we are having trouble with.

The screenshot can be viewed through this link:

https://cbsostorage.chem.umd.edu/owncloud/index.php/s/J5cKnOpCC4vb1VC



In the screenshot, the yellow color is the
anomalous map and a barium ion is fitted into
density near the positive green electron density.

The oligonucleotide was purchased from IDT. The
crystallization condition is 15% MPD, 120 mM
BaCl2, and 30 mM NaCaC pH 6.4. I have tried
modelling Ba2+ with coordinated waters, MPD, and
   

Re: [ccp4bb] AW: [ccp4bb] Unknown positive electron density

[Betty Chu]

Thank you all for your replies and suggestions.

I have fitted in some dummy waters as Herman suggested and this is the
result after one round of refinement. The waters are positioned where there
is highest electron density, but I am not sure how to move forward from
here.

https://cbsostorage.chem.umd.edu/owncloud/index.php/s/VTQ6Uinp1UVIWGR
https://cbsostorage.chem.umd.edu/owncloud/index.php/s/NUZKClayzSMn7PP
https://cbsostorage.chem.umd.edu/owncloud/index.php/s/0FZhxtgcQhhqnaA

I have also tried fitting in a nucleotide, but the geometry of it does not
fit the density well. We do not think this is due to Fourier truncation
ripples since the positive density is not at the crystallographic symmetry
axis.

Betty

On Tue, Aug 22, 2017 at 10:34 AM, Pradeep Pallan <pradeeppal...@gmail.com>
wrote:

> Hi Betty,
> Could you post a few more screen shots of different orientations of the
> electron density?
>
> If you see waters that are 1.6, 1.9 and 2.2 A away from the metal ion, I
> would try
> Mg2+ ion (trace amount of metal ions could be present in salt
> solutions/buffers as an impurity)
> and refine it (although 1.6Å is too close). In general, Mg2+ ions would
> show an octahedral
> geometry.
>
>
>
>
>
> On Tue, Aug 22, 2017 at 3:35 AM, <herman.schreu...@sanofi.com> wrote:
>
>> Dear Betty,
>>
>>
>>
>> You have very high resolution, which helps you to identify your ligand,
>> but the ligand may be disordered…
>>
>> What I would do is to place some dummy atoms (e.g. waters) and refine and
>> look if the molecule gets clearer. By scrolling the density in coot, you
>> can identify the positions with the highest electron density were you
>> should put your dummy atoms.
>>
>>
>>
>> Looking at your pictures, as far as is possible without the ability to
>> rotate them, I would try to fit deoxyribose-phosphate, or even a complete
>> nucleotide. Maybe your prep contained some unreacted nucleotides and your
>> anomalous peak is phosphorus.
>>
>>
>>
>> Good luck!
>>
>> Herman
>>
>>
>>
>> *Von:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *Im Auftrag
>> von *Betty Chu
>> *Gesendet:* Montag, 21. August 2017 17:19
>> *An:* CCP4BB@JISCMAIL.AC.UK
>> *Betreff:* [ccp4bb] Unknown positive electron density
>>
>>
>>
>> Dear ccp4bb,
>>
>> I am refining a 1.40 Angstrom data set for a DNA oligonucleotide. While
>> the model for the DNA fits very well into the density, there is a patch of
>> positive electron density in the solvent space that we are having trouble
>> with.
>>
>> The screenshot can be viewed through this link:
>> https://cbsostorage.chem.umd.edu/owncloud/index.php/s/J5cKnOpCC4vb1VC
>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__cbsostorage.chem.umd.edu_owncloud_index.php_s_J5cKnOpCC4vb1VC=DQMFaQ=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ=oUauCRPJVt0_cKdOakQvtJoEkS4gY9JlJmXfkd2GnlI=0XTzg6Yyi4dgz7G80vogTkpLLMZoM8fj53buMeenlJM=>
>>
>> In the screenshot, the yellow color is the anomalous map and a barium ion
>> is fitted into density near the positive green electron density.
>>
>>
>> The oligonucleotide was purchased from IDT. The crystallization condition
>> is 15% MPD, 120 mM BaCl2, and 30 mM NaCaC pH 6.4. I have tried modelling
>> Ba2+ with coordinated waters, MPD, and sodium cacodylate into the electron
>> density, but none of those fit well.
>>
>> Any suggestions regarding the identity of this electron density is much
>> appreciated. Thank you!
>>
>>
>>
>> Sincerely,
>>
>> Betty Chu
>>
>> Paukstelis Research Group
>>
>> Department of Chemistry and Biochemistry
>>
>> University of Maryland, College Park
>>
>
>
>
> --
>
> ---
> Pradeep Pallan
>

Re: [ccp4bb] AW: [ccp4bb] Unknown positive electron density

[Pradeep Pallan]

Hi Betty,
Could you post a few more screen shots of different orientations of the
electron density?

If you see waters that are 1.6, 1.9 and 2.2 A away from the metal ion, I
would try
Mg2+ ion (trace amount of metal ions could be present in salt
solutions/buffers as an impurity)
and refine it (although 1.6Å is too close). In general, Mg2+ ions would
show an octahedral
geometry.





On Tue, Aug 22, 2017 at 3:35 AM, <herman.schreu...@sanofi.com> wrote:

> Dear Betty,
>
>
>
> You have very high resolution, which helps you to identify your ligand,
> but the ligand may be disordered…
>
> What I would do is to place some dummy atoms (e.g. waters) and refine and
> look if the molecule gets clearer. By scrolling the density in coot, you
> can identify the positions with the highest electron density were you
> should put your dummy atoms.
>
>
>
> Looking at your pictures, as far as is possible without the ability to
> rotate them, I would try to fit deoxyribose-phosphate, or even a complete
> nucleotide. Maybe your prep contained some unreacted nucleotides and your
> anomalous peak is phosphorus.
>
>
>
> Good luck!
>
> Herman
>
>
>
> *Von:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *Im Auftrag von
> *Betty Chu
> *Gesendet:* Montag, 21. August 2017 17:19
> *An:* CCP4BB@JISCMAIL.AC.UK
> *Betreff:* [ccp4bb] Unknown positive electron density
>
>
>
> Dear ccp4bb,
>
> I am refining a 1.40 Angstrom data set for a DNA oligonucleotide. While
> the model for the DNA fits very well into the density, there is a patch of
> positive electron density in the solvent space that we are having trouble
> with.
>
> The screenshot can be viewed through this link:
> https://cbsostorage.chem.umd.edu/owncloud/index.php/s/J5cKnOpCC4vb1VC
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__cbsostorage.chem.umd.edu_owncloud_index.php_s_J5cKnOpCC4vb1VC=DQMFaQ=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ=oUauCRPJVt0_cKdOakQvtJoEkS4gY9JlJmXfkd2GnlI=0XTzg6Yyi4dgz7G80vogTkpLLMZoM8fj53buMeenlJM=>
>
> In the screenshot, the yellow color is the anomalous map and a barium ion
> is fitted into density near the positive green electron density.
>
>
> The oligonucleotide was purchased from IDT. The crystallization condition
> is 15% MPD, 120 mM BaCl2, and 30 mM NaCaC pH 6.4. I have tried modelling
> Ba2+ with coordinated waters, MPD, and sodium cacodylate into the electron
> density, but none of those fit well.
>
> Any suggestions regarding the identity of this electron density is much
> appreciated. Thank you!
>
>
>
> Sincerely,
>
> Betty Chu
>
> Paukstelis Research Group
>
> Department of Chemistry and Biochemistry
>
> University of Maryland, College Park
>



-- 

---
Pradeep Pallan

[ccp4bb] AW: [ccp4bb] Unknown positive electron density

[Herman . Schreuder]

Dear Betty,

You have very high resolution, which helps you to identify your ligand, but the 
ligand may be disordered…
What I would do is to place some dummy atoms (e.g. waters) and refine and look 
if the molecule gets clearer. By scrolling the density in coot, you can 
identify the positions with the highest electron density were you should put 
your dummy atoms.

Looking at your pictures, as far as is possible without the ability to rotate 
them, I would try to fit deoxyribose-phosphate, or even a complete nucleotide. 
Maybe your prep contained some unreacted nucleotides and your anomalous peak is 
phosphorus.

Good luck!
Herman

Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Betty Chu
Gesendet: Montag, 21. August 2017 17:19
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [ccp4bb] Unknown positive electron density

Dear ccp4bb,
I am refining a 1.40 Angstrom data set for a DNA oligonucleotide. While the 
model for the DNA fits very well into the density, there is a patch of positive 
electron density in the solvent space that we are having trouble with.

The screenshot can be viewed through this link:
https://cbsostorage.chem.umd.edu/owncloud/index.php/s/J5cKnOpCC4vb1VC<https://urldefense.proofpoint.com/v2/url?u=https-3A__cbsostorage.chem.umd.edu_owncloud_index.php_s_J5cKnOpCC4vb1VC=DQMFaQ=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ=oUauCRPJVt0_cKdOakQvtJoEkS4gY9JlJmXfkd2GnlI=0XTzg6Yyi4dgz7G80vogTkpLLMZoM8fj53buMeenlJM=>

In the screenshot, the yellow color is the anomalous map and a barium ion is 
fitted into density near the positive green electron density.

The oligonucleotide was purchased from IDT. The crystallization condition is 
15% MPD, 120 mM BaCl2, and 30 mM NaCaC pH 6.4. I have tried modelling Ba2+ with 
coordinated waters, MPD, and sodium cacodylate into the electron density, but 
none of those fit well.
Any suggestions regarding the identity of this electron density is much 
appreciated. Thank you!

Sincerely,
Betty Chu
Paukstelis Research Group
Department of Chemistry and Biochemistry
University of Maryland, College Park

Re: [ccp4bb] Unknown positive electron density

[Shailesh Tripathi]

Ionic Ba2+ has smaller radius 2/3 of metalic Ba. So it will have increased
e/A3 and modelling Ba atom might give positive density centered at Ba site.
This discussion might help:

http://ccp4bb.blogspot.in/2011/11/atomic-scattering-factors-in-refmac.html


Shailesh Kumar Tripathi,
Phone: 9686289668


On Tue, Aug 22, 2017 at 5:32 AM, Keller, Jacob <kell...@janelia.hhmi.org>
wrote:

> Fourier truncation ripples?
>
>
>
> JPK
>
>
>
> *From:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *On Behalf Of 
> *CRAIG
> A BINGMAN
> *Sent:* Monday, August 21, 2017 6:20 PM
> *To:* CCP4BB@JISCMAIL.AC.UK
> *Subject:* Re: [ccp4bb] Unknown positive electron density
>
>
>
> Betty,
>
>
>
> I think that f’’ for Ba at this wavelength is around 3.5 electrons, and
> f'' for As is expected to be about 3 electrons. Is there a nearby
> crystallographic symmetry axis?
>
>
>
> Craig
>
>
>
> On Aug 21, 2017, at 5:05 PM, Betty Chu <chube...@umd.edu> wrote:
>
>
>
> Hi Craig,
>
> The data collection wavelength was 0.92 Angstroms. Since we observe
> anomalous signal for Ba at this wavelength, we would expect greater
> anomalous signal if As were present. There is a possibility for weak
> anomalous signal in this positive density, but the weak anomalous signal
> only shows up if I try to model a Ba in the density. Without modelling
> anything, there is no anomalous signal.
>
> This is what the map looks like after one round of refinement with the Ba
> in the density. But since there are waters that are 1.6 Angstroms, 1.9
> Angstroms, and 2.2 Angstroms away from the Ba, which is smaller than the
> coordination distance between Ba and water, we are skeptical of the Ba
> being there.
>
> https://cbsostorage.chem.umd.edu/owncloud/index.php/s/O4lI2iKvRsQUoRo
>
>
> Thank you,
>
> Betty
>
>
>
> On Mon, Aug 21, 2017 at 5:21 PM, CRAIG A BINGMAN <cabing...@wisc.edu>
> wrote:
>
> What is the data collection wavelength/energy? Would you expect
> significant anomalous diffraction from As at this wavelength?
>
>
>
> On Aug 21, 2017, at 11:37 AM, Betty Chu <chube...@umd.edu> wrote:
>
>
>
> Hi Shailesh,
>
> When I modelled in the Barium ion with octahedrally coordinated waters and
> ran the refinement, the distances from the barium to some of the waters
> ended up being too close (<2.2 Angstroms). Also, the positive electron
> density is connected. If the density indicated barium with coordinated
> waters, would that mean there are multiple ones present in the positive
> density?
>
> Here are more views of the connected positive density.
>
>
> https://cbsostorage.chem.umd.edu/owncloud/index.php/s/j5CgZIJe6NKgUlZ
>
> https://cbsostorage.chem.umd.edu/owncloud/index.php/s/YbiNFbT8AW1iHUQ
>
>
>
> On Mon, Aug 21, 2017 at 12:00 PM, Shailesh Tripathi <shailes...@gmail.com>
> wrote:
>
> Looks like Ba2+. Since it exist with coordination number 6 or above check
> what geometry water is following there (trigonal bipiramidal or so on).
> Water might also be shared by symmetry related Ba cation.
>
>
>
>
>
>
> Shailesh Kumar Tripathi,
>
> Phone: 9686289668
>
>
>
>
>
> On Mon, Aug 21, 2017 at 9:17 PM, Betty Chu <chube...@umd.edu> wrote:
>
> Yes, I have. The cacodylate ion does not fit well into the density.
>
>
>
> On Mon, Aug 21, 2017 at 11:44 AM, Pradeep Pallan <pradeeppal...@gmail.com>
> wrote:
>
> Did you try modelling in a cacodylate ion (CH3)2AsO2-?
>
>
>
> On Mon, Aug 21, 2017 at 10:19 AM, Betty Chu <chube...@umd.edu> wrote:
>
> Dear ccp4bb,
>
> I am refining a 1.40 Angstrom data set for a DNA oligonucleotide. While
> the model for the DNA fits very well into the density, there is a patch of
> positive electron density in the solvent space that we are having trouble
> with.
>
> The screenshot can be viewed through this link:
> https://cbsostorage.chem.umd.edu/owncloud/index.php/s/J5cKnOpCC4vb1VC
>
> In the screenshot, the yellow color is the anomalous map and a barium ion
> is fitted into density near the positive green electron density.
>
>
> The oligonucleotide was purchased from IDT. The crystallization condition
> is 15% MPD, 120 mM BaCl2, and 30 mM NaCaC pH 6.4. I have tried modelling
> Ba2+ with coordinated waters, MPD, and sodium cacodylate into the electron
> density, but none of those fit well.
>
> Any suggestions regarding the identity of this electron density is much
> appreciated. Thank you!
>
>
>
> Sincerely,
>
> Betty Chu
>
> Paukstelis Research Group
>
> Department of Chemistry and Biochemistry
>
> University of Maryland, College Park
>
>
>
>
>
> --
>
>
> ---
> Pradeep Pallan
>
>
>
>
>
>
>
>
>
>
>
>
>

Re: [ccp4bb] Unknown positive electron density

[Keller, Jacob]

Fourier truncation ripples?

JPK

From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of CRAIG A 
BINGMAN
Sent: Monday, August 21, 2017 6:20 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Unknown positive electron density

Betty,

I think that f’’ for Ba at this wavelength is around 3.5 electrons, and f'' for 
As is expected to be about 3 electrons. Is there a nearby crystallographic 
symmetry axis?

Craig

On Aug 21, 2017, at 5:05 PM, Betty Chu 
<chube...@umd.edu<mailto:chube...@umd.edu>> wrote:

Hi Craig,
The data collection wavelength was 0.92 Angstroms. Since we observe anomalous 
signal for Ba at this wavelength, we would expect greater anomalous signal if 
As were present. There is a possibility for weak anomalous signal in this 
positive density, but the weak anomalous signal only shows up if I try to model 
a Ba in the density. Without modelling anything, there is no anomalous signal.

This is what the map looks like after one round of refinement with the Ba in 
the density. But since there are waters that are 1.6 Angstroms, 1.9 Angstroms, 
and 2.2 Angstroms away from the Ba, which is smaller than the coordination 
distance between Ba and water, we are skeptical of the Ba being there.

https://cbsostorage.chem.umd.edu/owncloud/index.php/s/O4lI2iKvRsQUoRo

Thank you,
Betty

On Mon, Aug 21, 2017 at 5:21 PM, CRAIG A BINGMAN 
<cabing...@wisc.edu<mailto:cabing...@wisc.edu>> wrote:
What is the data collection wavelength/energy? Would you expect significant 
anomalous diffraction from As at this wavelength?

On Aug 21, 2017, at 11:37 AM, Betty Chu 
<chube...@umd.edu<mailto:chube...@umd.edu>> wrote:

Hi Shailesh,
When I modelled in the Barium ion with octahedrally coordinated waters and ran 
the refinement, the distances from the barium to some of the waters ended up 
being too close (<2.2 Angstroms). Also, the positive electron density is 
connected. If the density indicated barium with coordinated waters, would that 
mean there are multiple ones present in the positive density?
Here are more views of the connected positive density.

https://cbsostorage.chem.umd.edu/owncloud/index.php/s/j5CgZIJe6NKgUlZ

https://cbsostorage.chem.umd.edu/owncloud/index.php/s/YbiNFbT8AW1iHUQ

On Mon, Aug 21, 2017 at 12:00 PM, Shailesh Tripathi 
<shailes...@gmail.com<mailto:shailes...@gmail.com>> wrote:
Looks like Ba2+. Since it exist with coordination number 6 or above check what 
geometry water is following there (trigonal bipiramidal or so on). Water might 
also be shared by symmetry related Ba cation.



Shailesh Kumar Tripathi,
Phone: 9686289668


On Mon, Aug 21, 2017 at 9:17 PM, Betty Chu 
<chube...@umd.edu<mailto:chube...@umd.edu>> wrote:
Yes, I have. The cacodylate ion does not fit well into the density.

On Mon, Aug 21, 2017 at 11:44 AM, Pradeep Pallan 
<pradeeppal...@gmail.com<mailto:pradeeppal...@gmail.com>> wrote:
Did you try modelling in a cacodylate ion (CH3)2AsO2-?

On Mon, Aug 21, 2017 at 10:19 AM, Betty Chu 
<chube...@umd.edu<mailto:chube...@umd.edu>> wrote:
Dear ccp4bb,
I am refining a 1.40 Angstrom data set for a DNA oligonucleotide. While the 
model for the DNA fits very well into the density, there is a patch of positive 
electron density in the solvent space that we are having trouble with.

The screenshot can be viewed through this link:
https://cbsostorage.chem.umd.edu/owncloud/index.php/s/J5cKnOpCC4vb1VC

In the screenshot, the yellow color is the anomalous map and a barium ion is 
fitted into density near the positive green electron density.

The oligonucleotide was purchased from IDT. The crystallization condition is 
15% MPD, 120 mM BaCl2, and 30 mM NaCaC pH 6.4. I have tried modelling Ba2+ with 
coordinated waters, MPD, and sodium cacodylate into the electron density, but 
none of those fit well.
Any suggestions regarding the identity of this electron density is much 
appreciated. Thank you!

Sincerely,
Betty Chu
Paukstelis Research Group
Department of Chemistry and Biochemistry
University of Maryland, College Park



--

---
Pradeep Pallan

Re: [ccp4bb] Unknown positive electron density

[CRAIG A BINGMAN]

Betty,

I think that f’’ for Ba at this wavelength is around 3.5 electrons, and f'' for 
As is expected to be about 3 electrons. Is there a nearby crystallographic 
symmetry axis?

Craig

On Aug 21, 2017, at 5:05 PM, Betty Chu 
> wrote:

Hi Craig,

The data collection wavelength was 0.92 Angstroms. Since we observe anomalous 
signal for Ba at this wavelength, we would expect greater anomalous signal if 
As were present. There is a possibility for weak anomalous signal in this 
positive density, but the weak anomalous signal only shows up if I try to model 
a Ba in the density. Without modelling anything, there is no anomalous signal.

This is what the map looks like after one round of refinement with the Ba in 
the density. But since there are waters that are 1.6 Angstroms, 1.9 Angstroms, 
and 2.2 Angstroms away from the Ba, which is smaller than the coordination 
distance between Ba and water, we are skeptical of the Ba being there.

https://cbsostorage.chem.umd.edu/owncloud/index.php/s/O4lI2iKvRsQUoRo

Thank you,
Betty

On Mon, Aug 21, 2017 at 5:21 PM, CRAIG A BINGMAN 
> wrote:
What is the data collection wavelength/energy? Would you expect significant 
anomalous diffraction from As at this wavelength?

On Aug 21, 2017, at 11:37 AM, Betty Chu 
> wrote:

Hi Shailesh,

When I modelled in the Barium ion with octahedrally coordinated waters and ran 
the refinement, the distances from the barium to some of the waters ended up 
being too close (<2.2 Angstroms). Also, the positive electron density is 
connected. If the density indicated barium with coordinated waters, would that 
mean there are multiple ones present in the positive density?

Here are more views of the connected positive density.

https://cbsostorage.chem.umd.edu/owncloud/index.php/s/j5CgZIJe6NKgUlZ

https://cbsostorage.chem.umd.edu/owncloud/index.php/s/YbiNFbT8AW1iHUQ

On Mon, Aug 21, 2017 at 12:00 PM, Shailesh Tripathi 
> wrote:
Looks like Ba2+. Since it exist with coordination number 6 or above check what 
geometry water is following there (trigonal bipiramidal or so on). Water might 
also be shared by symmetry related Ba cation.



Shailesh Kumar Tripathi,
Phone: 9686289668


On Mon, Aug 21, 2017 at 9:17 PM, Betty Chu 
> wrote:
Yes, I have. The cacodylate ion does not fit well into the density.

On Mon, Aug 21, 2017 at 11:44 AM, Pradeep Pallan 
> wrote:
Did you try modelling in a cacodylate ion (CH3)2AsO2-?

On Mon, Aug 21, 2017 at 10:19 AM, Betty Chu 
> wrote:
Dear ccp4bb,

I am refining a 1.40 Angstrom data set for a DNA oligonucleotide. While the 
model for the DNA fits very well into the density, there is a patch of positive 
electron density in the solvent space that we are having trouble with.

The screenshot can be viewed through this link:
https://cbsostorage.chem.umd.edu/owncloud/index.php/s/J5cKnOpCC4vb1VC

In the screenshot, the yellow color is the anomalous map and a barium ion is 
fitted into density near the positive green electron density.

The oligonucleotide was purchased from IDT. The crystallization condition is 
15% MPD, 120 mM BaCl2, and 30 mM NaCaC pH 6.4. I have tried modelling Ba2+ with 
coordinated waters, MPD, and sodium cacodylate into the electron density, but 
none of those fit well.

Any suggestions regarding the identity of this electron density is much 
appreciated. Thank you!

Sincerely,

Betty Chu
Paukstelis Research Group
Department of Chemistry and Biochemistry
University of Maryland, College Park



--

---
Pradeep Pallan

Re: [ccp4bb] Unknown positive electron density

[Betty Chu]

Hi Craig,

The data collection wavelength was 0.92 Angstroms. Since we observe
anomalous signal for Ba at this wavelength, we would expect greater
anomalous signal if As were present. There is a possibility for weak
anomalous signal in this positive density, but the weak anomalous signal
only shows up if I try to model a Ba in the density. Without modelling
anything, there is no anomalous signal.

This is what the map looks like after one round of refinement with the Ba
in the density. But since there are waters that are 1.6 Angstroms, 1.9
Angstroms, and 2.2 Angstroms away from the Ba, which is smaller than the
coordination distance between Ba and water, we are skeptical of the Ba
being there.

https://cbsostorage.chem.umd.edu/owncloud/index.php/s/O4lI2iKvRsQUoRo

Thank you,
Betty

On Mon, Aug 21, 2017 at 5:21 PM, CRAIG A BINGMAN  wrote:

> What is the data collection wavelength/energy? Would you expect
> significant anomalous diffraction from As at this wavelength?
>
> On Aug 21, 2017, at 11:37 AM, Betty Chu  wrote:
>
> Hi Shailesh,
>
> When I modelled in the Barium ion with octahedrally coordinated waters and
> ran the refinement, the distances from the barium to some of the waters
> ended up being too close (<2.2 Angstroms). Also, the positive electron
> density is connected. If the density indicated barium with coordinated
> waters, would that mean there are multiple ones present in the positive
> density?
>
> Here are more views of the connected positive density.
>
> https://cbsostorage.chem.umd.edu/owncloud/index.php/s/j5CgZIJe6NKgUlZ
>
> https://cbsostorage.chem.umd.edu/owncloud/index.php/s/YbiNFbT8AW1iHUQ
>
> On Mon, Aug 21, 2017 at 12:00 PM, Shailesh Tripathi 
> wrote:
>
>> Looks like Ba2+. Since it exist with coordination number 6 or above check
>> what geometry water is following there (trigonal bipiramidal or so on).
>> Water might also be shared by symmetry related Ba cation.
>>
>>
>>
>> Shailesh Kumar Tripathi,
>> Phone: 9686289668
>>
>>
>> On Mon, Aug 21, 2017 at 9:17 PM, Betty Chu  wrote:
>>
>>> Yes, I have. The cacodylate ion does not fit well into the density.
>>>
>>> On Mon, Aug 21, 2017 at 11:44 AM, Pradeep Pallan <
>>> pradeeppal...@gmail.com> wrote:
>>>
 Did you try modelling in a cacodylate ion (CH3)2AsO2-?

 On Mon, Aug 21, 2017 at 10:19 AM, Betty Chu  wrote:

> Dear ccp4bb,
>
> I am refining a 1.40 Angstrom data set for a DNA oligonucleotide.
> While the model for the DNA fits very well into the density, there is a
> patch of positive electron density in the solvent space that we are having
> trouble with.
>
> The screenshot can be viewed through this link:
> https://cbsostorage.chem.umd.edu/owncloud/index.php/s/J5cKnOpCC4vb1VC
>
> In the screenshot, the yellow color is the anomalous map and a barium
> ion is fitted into density near the positive green electron density.
>
> The oligonucleotide was purchased from IDT. The crystallization
> condition is 15% MPD, 120 mM BaCl2, and 30 mM NaCaC pH 6.4. I have tried
> modelling Ba2+ with coordinated waters, MPD, and sodium cacodylate into 
> the
> electron density, but none of those fit well.
>
> Any suggestions regarding the identity of this electron density is
> much appreciated. Thank you!
>
> Sincerely,
>
> Betty Chu
> Paukstelis Research Group
> Department of Chemistry and Biochemistry
> University of Maryland, College Park
>



 --

 ---
 Pradeep Pallan

>>>
>>>
>>
>
>

Re: [ccp4bb] Unknown positive electron density

[CRAIG A BINGMAN]

What is the data collection wavelength/energy? Would you expect significant 
anomalous diffraction from As at this wavelength?

On Aug 21, 2017, at 11:37 AM, Betty Chu 
> wrote:

Hi Shailesh,

When I modelled in the Barium ion with octahedrally coordinated waters and ran 
the refinement, the distances from the barium to some of the waters ended up 
being too close (<2.2 Angstroms). Also, the positive electron density is 
connected. If the density indicated barium with coordinated waters, would that 
mean there are multiple ones present in the positive density?

Here are more views of the connected positive density.

https://cbsostorage.chem.umd.edu/owncloud/index.php/s/j5CgZIJe6NKgUlZ

https://cbsostorage.chem.umd.edu/owncloud/index.php/s/YbiNFbT8AW1iHUQ

On Mon, Aug 21, 2017 at 12:00 PM, Shailesh Tripathi 
> wrote:
Looks like Ba2+. Since it exist with coordination number 6 or above check what 
geometry water is following there (trigonal bipiramidal or so on). Water might 
also be shared by symmetry related Ba cation.



Shailesh Kumar Tripathi,
Phone: 9686289668


On Mon, Aug 21, 2017 at 9:17 PM, Betty Chu 
> wrote:
Yes, I have. The cacodylate ion does not fit well into the density.

On Mon, Aug 21, 2017 at 11:44 AM, Pradeep Pallan 
> wrote:
Did you try modelling in a cacodylate ion (CH3)2AsO2-?

On Mon, Aug 21, 2017 at 10:19 AM, Betty Chu 
> wrote:
Dear ccp4bb,

I am refining a 1.40 Angstrom data set for a DNA oligonucleotide. While the 
model for the DNA fits very well into the density, there is a patch of positive 
electron density in the solvent space that we are having trouble with.

The screenshot can be viewed through this link:
https://cbsostorage.chem.umd.edu/owncloud/index.php/s/J5cKnOpCC4vb1VC

In the screenshot, the yellow color is the anomalous map and a barium ion is 
fitted into density near the positive green electron density.

The oligonucleotide was purchased from IDT. The crystallization condition is 
15% MPD, 120 mM BaCl2, and 30 mM NaCaC pH 6.4. I have tried modelling Ba2+ with 
coordinated waters, MPD, and sodium cacodylate into the electron density, but 
none of those fit well.

Any suggestions regarding the identity of this electron density is much 
appreciated. Thank you!

Sincerely,

Betty Chu
Paukstelis Research Group
Department of Chemistry and Biochemistry
University of Maryland, College Park



--

---
Pradeep Pallan

Re: [ccp4bb] Unknown positive electron density

[Betty Chu]

Hi Shailesh,

When I modelled in the Barium ion with octahedrally coordinated waters and
ran the refinement, the distances from the barium to some of the waters
ended up being too close (<2.2 Angstroms). Also, the positive electron
density is connected. If the density indicated barium with coordinated
waters, would that mean there are multiple ones present in the positive
density?

Here are more views of the connected positive density.

https://cbsostorage.chem.umd.edu/owncloud/index.php/s/j5CgZIJe6NKgUlZ

https://cbsostorage.chem.umd.edu/owncloud/index.php/s/YbiNFbT8AW1iHUQ

On Mon, Aug 21, 2017 at 12:00 PM, Shailesh Tripathi 
wrote:

> Looks like Ba2+. Since it exist with coordination number 6 or above check
> what geometry water is following there (trigonal bipiramidal or so on).
> Water might also be shared by symmetry related Ba cation.
>
>
>
> Shailesh Kumar Tripathi,
> Phone: 9686289668
>
>
> On Mon, Aug 21, 2017 at 9:17 PM, Betty Chu  wrote:
>
>> Yes, I have. The cacodylate ion does not fit well into the density.
>>
>> On Mon, Aug 21, 2017 at 11:44 AM, Pradeep Pallan > > wrote:
>>
>>> Did you try modelling in a cacodylate ion (CH3)2AsO2-?
>>>
>>> On Mon, Aug 21, 2017 at 10:19 AM, Betty Chu  wrote:
>>>
 Dear ccp4bb,

 I am refining a 1.40 Angstrom data set for a DNA oligonucleotide. While
 the model for the DNA fits very well into the density, there is a patch of
 positive electron density in the solvent space that we are having trouble
 with.

 The screenshot can be viewed through this link:
 https://cbsostorage.chem.umd.edu/owncloud/index.php/s/J5cKnOpCC4vb1VC

 In the screenshot, the yellow color is the anomalous map and a barium
 ion is fitted into density near the positive green electron density.

 The oligonucleotide was purchased from IDT. The crystallization
 condition is 15% MPD, 120 mM BaCl2, and 30 mM NaCaC pH 6.4. I have tried
 modelling Ba2+ with coordinated waters, MPD, and sodium cacodylate into the
 electron density, but none of those fit well.

 Any suggestions regarding the identity of this electron density is much
 appreciated. Thank you!

 Sincerely,

 Betty Chu
 Paukstelis Research Group
 Department of Chemistry and Biochemistry
 University of Maryland, College Park

>>>
>>>
>>>
>>> --
>>>
>>> ---
>>> Pradeep Pallan
>>>
>>
>>
>

Re: [ccp4bb] Unknown positive electron density

[Shailesh Tripathi]

Looks like Ba2+. Since it exist with coordination number 6 or above check
what geometry water is following there (trigonal bipiramidal or so on).
Water might also be shared by symmetry related Ba cation.



Shailesh Kumar Tripathi,
Phone: 9686289668


On Mon, Aug 21, 2017 at 9:17 PM, Betty Chu  wrote:

> Yes, I have. The cacodylate ion does not fit well into the density.
>
> On Mon, Aug 21, 2017 at 11:44 AM, Pradeep Pallan 
> wrote:
>
>> Did you try modelling in a cacodylate ion (CH3)2AsO2-?
>>
>> On Mon, Aug 21, 2017 at 10:19 AM, Betty Chu  wrote:
>>
>>> Dear ccp4bb,
>>>
>>> I am refining a 1.40 Angstrom data set for a DNA oligonucleotide. While
>>> the model for the DNA fits very well into the density, there is a patch of
>>> positive electron density in the solvent space that we are having trouble
>>> with.
>>>
>>> The screenshot can be viewed through this link:
>>> https://cbsostorage.chem.umd.edu/owncloud/index.php/s/J5cKnOpCC4vb1VC
>>>
>>> In the screenshot, the yellow color is the anomalous map and a barium
>>> ion is fitted into density near the positive green electron density.
>>>
>>> The oligonucleotide was purchased from IDT. The crystallization
>>> condition is 15% MPD, 120 mM BaCl2, and 30 mM NaCaC pH 6.4. I have tried
>>> modelling Ba2+ with coordinated waters, MPD, and sodium cacodylate into the
>>> electron density, but none of those fit well.
>>>
>>> Any suggestions regarding the identity of this electron density is much
>>> appreciated. Thank you!
>>>
>>> Sincerely,
>>>
>>> Betty Chu
>>> Paukstelis Research Group
>>> Department of Chemistry and Biochemistry
>>> University of Maryland, College Park
>>>
>>
>>
>>
>> --
>>
>> ---
>> Pradeep Pallan
>>
>
>

Re: [ccp4bb] Unknown positive electron density

[Betty Chu]

Yes, I have. The cacodylate ion does not fit well into the density.

On Mon, Aug 21, 2017 at 11:44 AM, Pradeep Pallan 
wrote:

> Did you try modelling in a cacodylate ion (CH3)2AsO2-?
>
> On Mon, Aug 21, 2017 at 10:19 AM, Betty Chu  wrote:
>
>> Dear ccp4bb,
>>
>> I am refining a 1.40 Angstrom data set for a DNA oligonucleotide. While
>> the model for the DNA fits very well into the density, there is a patch of
>> positive electron density in the solvent space that we are having trouble
>> with.
>>
>> The screenshot can be viewed through this link:
>> https://cbsostorage.chem.umd.edu/owncloud/index.php/s/J5cKnOpCC4vb1VC
>>
>> In the screenshot, the yellow color is the anomalous map and a barium ion
>> is fitted into density near the positive green electron density.
>>
>> The oligonucleotide was purchased from IDT. The crystallization condition
>> is 15% MPD, 120 mM BaCl2, and 30 mM NaCaC pH 6.4. I have tried modelling
>> Ba2+ with coordinated waters, MPD, and sodium cacodylate into the electron
>> density, but none of those fit well.
>>
>> Any suggestions regarding the identity of this electron density is much
>> appreciated. Thank you!
>>
>> Sincerely,
>>
>> Betty Chu
>> Paukstelis Research Group
>> Department of Chemistry and Biochemistry
>> University of Maryland, College Park
>>
>
>
>
> --
>
> ---
> Pradeep Pallan
>

Re: [ccp4bb] Unknown positive electron density

[Pradeep Pallan]

Did you try modelling in a cacodylate ion (CH3)2AsO2-?

On Mon, Aug 21, 2017 at 10:19 AM, Betty Chu  wrote:

> Dear ccp4bb,
>
> I am refining a 1.40 Angstrom data set for a DNA oligonucleotide. While
> the model for the DNA fits very well into the density, there is a patch of
> positive electron density in the solvent space that we are having trouble
> with.
>
> The screenshot can be viewed through this link:
> https://cbsostorage.chem.umd.edu/owncloud/index.php/s/J5cKnOpCC4vb1VC
>
> In the screenshot, the yellow color is the anomalous map and a barium ion
> is fitted into density near the positive green electron density.
>
> The oligonucleotide was purchased from IDT. The crystallization condition
> is 15% MPD, 120 mM BaCl2, and 30 mM NaCaC pH 6.4. I have tried modelling
> Ba2+ with coordinated waters, MPD, and sodium cacodylate into the electron
> density, but none of those fit well.
>
> Any suggestions regarding the identity of this electron density is much
> appreciated. Thank you!
>
> Sincerely,
>
> Betty Chu
> Paukstelis Research Group
> Department of Chemistry and Biochemistry
> University of Maryland, College Park
>



-- 

---
Pradeep Pallan

[ccp4bb] Unknown positive electron density

[Betty Chu]

Dear ccp4bb,

I am refining a 1.40 Angstrom data set for a DNA oligonucleotide. While the
model for the DNA fits very well into the density, there is a patch of
positive electron density in the solvent space that we are having trouble
with.

The screenshot can be viewed through this link:
https://cbsostorage.chem.umd.edu/owncloud/index.php/s/J5cKnOpCC4vb1VC

In the screenshot, the yellow color is the anomalous map and a barium ion
is fitted into density near the positive green electron density.

The oligonucleotide was purchased from IDT. The crystallization condition
is 15% MPD, 120 mM BaCl2, and 30 mM NaCaC pH 6.4. I have tried modelling
Ba2+ with coordinated waters, MPD, and sodium cacodylate into the electron
density, but none of those fit well.

Any suggestions regarding the identity of this electron density is much
appreciated. Thank you!

Sincerely,

Betty Chu
Paukstelis Research Group
Department of Chemistry and Biochemistry
University of Maryland, College Park