[ccp4bb] MX Tutorials satellite to ESRF User Meeting 2021

[Daniele de Sanctis]

Dear colleagues,

we would like to draw your attention to two Tutorials that are organized
satellite to the virtual ESRF User Meeting 2021 that might be of your
interest: *Remote data collection with EXI and MXCuBE3 *and* Getting the
best out of MASSIF-1 and workflows at the ESRF*

The registration to the user meeting is open until the 4th of February
https://events.esrf.fr/misapps/workshops-web/index.jsp .
The two tutorials will be held on zoom on Monday 8 February, more
information is available at the event web page
https://www.esrf.eu/UM2021/Tutorials

Hope to see you there

Daniele, Gianluca, Didier, Matthew

-- 

ἀρετή
---
Daniele de Sanctis
Structural Biology Group
ESRF - The European Synchrotron
Grenoble, France
Tel 33 (0)4 76 88 2869

http://www.esrf.eu/id29



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[ccp4bb] Elemental Analysis

[Andrew Lovering]

Dear CCP4ers

We have a protein with moderate resolution (mid 2s) with obvious metal ion 
density holding the oligomer together. We can make an educated guess that the 
ions are likely to be Mg/Ca and can look at co-ordination and bond 
lengths.but I have a more specific question - would it be appropriate to 
try and identify these at the beamline? Obviously the edges for these aren't 
accessible to sit either side of the peak but perhaps something like micro-pixe 
would be fun; is this done routinely?
https://doi.org/10.1016/j.pbiomolbio.2004.09.005

Best & thanks in advance
Andy




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Re: [ccp4bb] Elemental Analysis

[Jon Cooper]

Hello, there is atomic-absorption. Breaks your heart to see the protein going 
into the flame, but we got good results for Se and transition metals with a 
superoxide dismutase. I doubt if there'll ever be one of those on a beam line 
;-0 Cheers, Jon Cooper.

Sent from ProtonMail mobile

 Original Message 
On 7 Jan 2021, 14:13, Andrew Lovering wrote:

> Dear CCP4ers
>
> We have a protein with moderate resolution (mid 2s) with obvious metal ion 
> density holding the oligomer together. We can make an educated guess that the 
> ions are likely to be Mg/Ca and can look at co-ordination and bond 
> lengths…..but I have a more specific question – would it be appropriate to 
> try and identify these at the beamline? Obviously the edges for these aren’t 
> accessible to sit either side of the peak but perhaps something like 
> micro-pixe would be fun; is this done routinely?
>
> https://doi.org/10.1016/j.pbiomolbio.2004.09.005
>
> Best & thanks in advance
>
> Andy
>
> ---
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1



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Re: [ccp4bb] Elemental Analysis

[Jon Cooper]

Hello again, re: amount, yes, from memory, it was a few milligrams. We also 
used EDAX on dried samples IIRC. Cheers, Jon.C.

Sent from ProtonMail mobile

 Original Message 
On 7 Jan 2021, 14:13, Andrew Lovering wrote:

> Dear CCP4ers
>
> We have a protein with moderate resolution (mid 2s) with obvious metal ion 
> density holding the oligomer together. We can make an educated guess that the 
> ions are likely to be Mg/Ca and can look at co-ordination and bond 
> lengths…..but I have a more specific question – would it be appropriate to 
> try and identify these at the beamline? Obviously the edges for these aren’t 
> accessible to sit either side of the peak but perhaps something like 
> micro-pixe would be fun; is this done routinely?
>
> https://doi.org/10.1016/j.pbiomolbio.2004.09.005
>
> Best & thanks in advance
>
> Andy
>
> ---
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1



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Re: [ccp4bb] Elemental Analysis

[Edward Snell]

Hi Andrew,

We had considerable success with MicroPIXE collaborating with the Garman group 
in Oxford and the Surrey Ion Beam Center. There is a tiny amount of sample 
needed, it's an atomic technique so the sample can be from that old tube that 
hadn't been discarded yet, and it provides identification and with a little 
care, stoichiometry. At the risk of blowing our own horn we have a paper on 
this in the Journal of the American Chemical Society that is public access, 
Grime et al., High-Throughput PIXE as an essential quantitative assay for 
accurate metalloprotein structural analysis: Development and application, 
142,1, 185-197.  It is publicly available at 
https://pubs.acs.org/doi/abs/10.1021/jacs.9b09186 and contains citations to the 
major papers in the field. We were able to use it to identify a previously 
unidentified metal modeled as a water cluster and from that produce a model of 
the actual ligand that was present.

Best,

Eddie

https://getacrystal.org - The High-throughput Crystallization Screening Center

Edward Snell Ph.D.

President and CEO | Hauptman-Woodward Medical Research Institute
Director | NSF BioXFEL Science and Technology Center
BioInnovations Chaired Professorship | University at Buffalo, SUNY

p: +1 716 898 8631 | f: +1 716 898 8660
e: esn...@hwi.buffalo.edu
skype: eddie.snell

Hauptman-Woodward Medical Research Institute
700 Ellicott Street | Buffalo, NY 14203-1102
hwi.buffalo.edu


[hwi-logo-primary-horizontal]





From: CCP4 bulletin board  On Behalf Of Andrew Lovering
Sent: Thursday, January 7, 2021 9:13 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Elemental Analysis

Dear CCP4ers   We have a protein with moderate resolution (mid 2s) with obvious 
metal ion density holding the oligomer together. We can make an educated guess 
that the ions are likely to be Mg/Ca
This sender is trusted.

sophospsmartbannerend
Dear CCP4ers

We have a protein with moderate resolution (mid 2s) with obvious metal ion 
density holding the oligomer together. We can make an educated guess that the 
ions are likely to be Mg/Ca and can look at co-ordination and bond 
lengths.but I have a more specific question - would it be appropriate to 
try and identify these at the beamline? Obviously the edges for these aren't 
accessible to sit either side of the peak but perhaps something like micro-pixe 
would be fun; is this done routinely?
https://doi.org/10.1016/j.pbiomolbio.2004.09.005

Best & thanks in advance
Andy




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[ccp4bb] Elemental Analysis

[Elspeth Garman]

Dear Andy
Yes! I have regular runs of micro-PIXE. Happy to discuss with you off line.
Best wishes
Elspeth

From: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK>> 
On Behalf Of Andrew Lovering
Sent: 07 January 2021 14:13
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Elemental Analysis

Dear CCP4ers

We have a protein with moderate resolution (mid 2s) with obvious metal ion 
density holding the oligomer together. We can make an educated guess that the 
ions are likely to be Mg/Ca and can look at co-ordination and bond 
lengths.but I have a more specific question - would it be appropriate to 
try and identify these at the beamline? Obviously the edges for these aren't 
accessible to sit either side of the peak but perhaps something like micro-pixe 
would be fun; is this done routinely?
https://doi.org/10.1016/j.pbiomolbio.2004.09.005

Best & thanks in advance
Andy




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Re: [ccp4bb] Elemental Analysis

[Sarah Bowman]

Hi Andy,

We were able to use EDX fluorescence scans at a beam line to detect calcium in 
crystals.

https://pubmed.ncbi.nlm.nih.gov/29890074/

It isn't quantitative like micro-pixe but you can see it...

Eddie Snell and Elspeth Garman and team have done some further work on 
micro-pixe, as well – very cool stuff!

https://pubmed.ncbi.nlm.nih.gov/31794207/

Cheers,
Sarah

Sarah EJ Bowman PhD
Associate Research Scientist | Hauptman-Woodward Medical Research Institute
Director | High-Throughput Crystallization Screening Center
Research Associate Professor | Department of Biochemistry | University at 
Buffalo

p: +1 716 898 8623
e: sbowman at hwi.buffalo.edu

Research Webpage
Crystallization Center Webpage

Hauptman-Woodward Medical Research Institute
700 Ellicott Street | Buffalo, NY 14203

From: CCP4 bulletin board  on behalf of Andrew Lovering 

Reply-To: Andrew Lovering 
Date: Thursday, January 7, 2021 at 9:13 AM
To: "CCP4BB@JISCMAIL.AC.UK" 
Subject: Elemental Analysis

Dear CCP4ers   We have a protein with moderate resolution (mid 2s) with obvious 
metal ion density holding the oligomer together. We can make an educated guess 
that the ions are likely to be Mg/Ca
This sender is trusted.

sophospsmartbannerend
Dear CCP4ers

We have a protein with moderate resolution (mid 2s) with obvious metal ion 
density holding the oligomer together. We can make an educated guess that the 
ions are likely to be Mg/Ca and can look at co-ordination and bond 
lengths…..but I have a more specific question – would it be appropriate to try 
and identify these at the beamline? Obviously the edges for these aren’t 
accessible to sit either side of the peak but perhaps something like micro-pixe 
would be fun; is this done routinely?
https://doi.org/10.1016/j.pbiomolbio.2004.09.005

Best & thanks in advance
Andy




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Re: [ccp4bb] Elemental Analysis

[El Omari, Kamel (DLSLtd,RAL,LSCI)]

Dear Andy,

We can easily reach the Ca absorption edge on I23 (Diamond long wavelength 
beamline), so we can tell you if you have calcium in your crystal but also its 
location.
Have a look at the beamline webpage:
https://www.diamond.ac.uk/Instruments/Mx/I23.html
Cheers,
Kamel

From: CCP4 bulletin board  on behalf of Andrew Lovering 

Sent: 07 January 2021 14:13
To: CCP4BB@JISCMAIL.AC.UK 
Subject: [ccp4bb] Elemental Analysis


Dear CCP4ers



We have a protein with moderate resolution (mid 2s) with obvious metal ion 
density holding the oligomer together. We can make an educated guess that the 
ions are likely to be Mg/Ca and can look at co-ordination and bond 
lengths…..but I have a more specific question – would it be appropriate to try 
and identify these at the beamline? Obviously the edges for these aren’t 
accessible to sit either side of the peak but perhaps something like micro-pixe 
would be fun; is this done routinely?

https://doi.org/10.1016/j.pbiomolbio.2004.09.005



Best & thanks in advance

Andy





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

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Re: [ccp4bb] Elemental Analysis

[Sarah Bowman]

As a follow-up, we have a postdoc position open to further develop metal 
identification methods for crystals and in solution!

The project: structural study of biological systems that are impacted by free 
radical activity and metalloproteins, where the modeled metal and/or 
coordination state are of interest for further investigation. The work will use 
X-ray crystallography, UV-spectroscopy, and micro-PIXE techniques. The eventual 
aim involves structural studies using X-ray free-electron sources for radiation 
chemistry-free data. It is possible that neutron studies would also take place.

The position will be based at HWI through the University at Buffalo in the 
Snell and 
Bowman laboratories.  
More details.

Happy New Year!
Sarah

Sarah EJ Bowman PhD
Associate Research Scientist | Hauptman-Woodward Medical Research Institute
Director | High-Throughput Crystallization Screening Center
Research Associate Professor | Department of Biochemistry | University at 
Buffalo

p: +1 716 898 8623
e: sbowman at hwi.buffalo.edu

Research Webpage
www.getacrystal.org

Hauptman-Woodward Medical Research Institute
700 Ellicott Street | Buffalo, NY 14203

From: CCP4 bulletin board  on behalf of Sarah Bowman 

Reply-To: Sarah Bowman 
Date: Thursday, January 7, 2021 at 9:52 AM
To: "CCP4BB@JISCMAIL.AC.UK" 
Subject: Re: Elemental Analysis

Hi Andy,   We were able to use EDX fluorescence scans at a beam line to detect 
calcium in crystals.   https://pubmed.ncbi.nlm.nih.gov/29890074/   It isn't 
quantitative like micro-pixe b
This sender is trusted.

sophospsmartbannerend
Hi Andy,

We were able to use EDX fluorescence scans at a beam line to detect calcium in 
crystals.

https://pubmed.ncbi.nlm.nih.gov/29890074/

It isn't quantitative like micro-pixe but you can see it...

Eddie Snell and Elspeth Garman and team have done some further work on 
micro-pixe, as well – very cool stuff!

https://pubmed.ncbi.nlm.nih.gov/31794207/

Cheers,
Sarah

Sarah EJ Bowman PhD
Associate Research Scientist | Hauptman-Woodward Medical Research Institute
Director | High-Throughput Crystallization Screening Center
Research Associate Professor | Department of Biochemistry | University at 
Buffalo

p: +1 716 898 8623
e: sbowman at hwi.buffalo.edu

Research Webpage
Crystallization Center Webpage

Hauptman-Woodward Medical Research Institute
700 Ellicott Street | Buffalo, NY 14203

From: CCP4 bulletin board  on behalf of Andrew Lovering 

Reply-To: Andrew Lovering 
Date: Thursday, January 7, 2021 at 9:13 AM
To: "CCP4BB@JISCMAIL.AC.UK" 
Subject: Elemental Analysis

Dear CCP4ers   We have a protein with moderate resolution (mid 2s) with obvious 
metal ion density holding the oligomer together. We can make an educated guess 
that the ions are likely to be Mg/Ca
This sender is trusted.

sophospsmartbannerend
Dear CCP4ers

We have a protein with moderate resolution (mid 2s) with obvious metal ion 
density holding the oligomer together. We can make an educated guess that the 
ions are likely to be Mg/Ca and can look at co-ordination and bond 
lengths…..but I have a more specific question – would it be appropriate to try 
and identify these at the beamline? Obviously the edges for these aren’t 
accessible to sit either side of the peak but perhaps something like micro-pixe 
would be fun; is this done routinely?
https://doi.org/10.1016/j.pbiomolbio.2004.09.005

Best & thanks in advance
Andy




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[ccp4bb] Post-doc position - Columbia University

[Liang Tong]

A Post-doctoral Research Associate position is available for structural
studies on proteins involved in RNA processing and quality control, using
cryo-EM and crystallography. We have extensive experience in these areas,
and have generated many high-impact publications (for example Science, 367,
700, 2020; Mol. Cell, 77, 800, 2020). Please see our home page for more
information-



http://tonglab.biology.columbia.edu/


Strong experience in protein biochemistry is required. Prior experience
with cryo-EM and/or X-ray crystallography is desirable.


Please send CV and names of three references to me by email.


Liang Tong

Department of Biological Sciences
Columbia University
New York, NY 10027
Email: lt...@columbia.edu



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