[ccp4bb] Call for Stanford-SLAC Cryo-EM Center (S2C2) Proposals

[Dunn, Lisa B.]

Dear All,

June 1 is the next deadline for submitting project proposals to the 
Stanford-SLAC Cryo-EM Center (S2C2).  Please apply at  
https://userportal.slac.stanford.edu/

More information about the S2C2 program and the project application process is 
available at:  https://cryoem.slac.stanford.edu/s2c2/

Best regards,

Lisa Dunn
Stanford-SLAC Cryo-EM Center (S2C2)
SLAC National Accelerator Laboratory
2575 Sand Hill Rd.
Menlo Park, CA 94025
l...@slac.stanford.edu




To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1

Re: [ccp4bb] A Question about crystal packing

[Jonathan Cooper]

Hello, can you use the pisa server or similar to compare the extent of 
domain-domain and domain-DNA contacts versus crystal contacts in your 
structures? It might help to show which is the dominant factor affecting domain 
orientation. 
Sent from Yahoo Mail on Android 
 
  On Tue, 28 May 2019 at 14:45, Zizi Tian<18311218...@163.com> wrote:   Hi 
All,I has recently solved my X-ray structures of the ZnF domains of Bo and its 
complex with dsDNA. A structural comparison of holo-Bo and the Bo-DNA binary 
complex reveals that the relative orientation of domains ZnF3 undergoes a 
rotation of 50.5 degrees Does anyone know how to show there are no effects of 
the crystal packing .
 Please help me in this regard. 
 Best regards




At 2019-05-28 20:55:07, "Anamika Singh"  wrote:
 
Hi All,

Does anyone know what is the actual difference between CIP and EDTA method for 
exchanging the GppNHp (non-hydrolysable GTP) or GDP with the purified RAS 
protein?


I have a protocol according to which I need to incubate the purified RAS with 
GppNHp having 20U of alkaline phosphatase, 10uM of Zinc Chloride and 200mM 
ammonium sulfate for 2 hr at room temperature. In this protocol, they have 
mentioned that ammonium sulfate needs to be added in the last. I am quite 
confused, according to them do I need to add it after 2 hrs incubation or I 
have to add this at last to the mixture of (purified RAS+GppNHp+Zinc chloride 
and alkaline phosphatase)?
Since this protein and its mechanism is new to me so not sure what to do. After 
reading some papers also I am not able to understand which method is good for 
exchange and how these reactions behave? 
Please help me in this regard.

-- 
Anamika Singh
Post-Doctoral FellowSilberman Institute of Life Sciences Hebrew University of 
Jerusalem, IsraelNo: 054-294-8036

To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1





 


To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
  



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1

Re: [ccp4bb] A Question about crystal packing

[Patrick Loll]

It is very difficult to demonstrate rigorously that crystal packing does not 
favor a particular conformation. If you can show that the same conformation 
occurs in solution (SAXS, NMR), or that the same conformation is found in a 
different space group with different packing, then you have a pretty conclusive 
answer. Obviously this involves a great deal of extra effort.

> On 28 May 2019, at 9:59 AM, Zizi Tian <18311218...@163.com> wrote:
> 
> Hi All,
> I has recently solved my X-ray structures of the ZnF domains of protein and 
> its complex with dsDNA. A structural comparison of holo-protein and the 
> protein-DNA binary complex reveals that the relative orientation of domains 
> ZnF3 undergoes a rotation of 50.5 degrees Does anyone know how to show there 
> are no effects of the crystal packing .
> 
>  Please help me in this regard. 
> 
>  Best regard
> 
> 
> 
> 
> 
>  
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 
> 
Patrick Loll
pjl...@gmail.com






To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1

Re: [ccp4bb] A Question about crystal packing

[Zizi Tian]

Hi All,
I has recently solved my X-ray structures of the ZnF domains of protein and its 
complex with dsDNA. A structural comparison of holo-protein and the protein-DNA 
binary complex reveals that the relative orientation of domains ZnF3 undergoes 
a rotation of 50.5 degrees Does anyone know how to show there are no effects of 
the crystal packing .


 Please help me in this regard. 


 Best regard






To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1

[ccp4bb] A Question about crystal packing

[Zizi Tian]

Hi All,
I has recently solved my X-ray structures of the ZnF domains of Bo and its 
complex with dsDNA. A structural comparison of holo-Bo and the Bo-DNA binary 
complex reveals that the relative orientation of domains ZnF3 undergoes a 
rotation of 50.5 degrees Does anyone know how to show there are no effects of 
the crystal packing .


 Please help me in this regard. 


 Best regards






At 2019-05-28 20:55:07, "Anamika Singh"  wrote:

Hi All,


Does anyone know what is the actual difference between CIP and EDTA method for 
exchanging the GppNHp (non-hydrolysable GTP) or GDP with the purified RAS 
protein?



I have a protocol according to which I need to incubate the purified RAS with 
GppNHp having 20U of alkaline phosphatase, 10uM of Zinc Chloride and 200mM 
ammonium sulfate for 2 hr at room temperature. In this protocol, they have 
mentioned that ammonium sulfate needs to be added in the last. I am quite 
confused, according to them do I need to add it after 2 hrs incubation or I 
have to add this at last to the mixture of (purified RAS+GppNHp+Zinc chloride 
and alkaline phosphatase)?


Since this protein and its mechanism is new to me so not sure what to do. After 
reading some papers also I am not able to understand which method is good for 
exchange and how these reactions behave? 


Please help me in this regard.



--

Anamika Singh
Post-Doctoral Fellow
Silberman Institute of Life Sciences 
Hebrew University of Jerusalem, Israel
No: 054-294-8036



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1

Re: [ccp4bb] Question on author provided HELIX/SHEET records and assignment of a continuous helix that changes its helix class.

[Jonathan Cooper]

Re: question 2, for simplicity, I would call it all one helix and regard the 
3-10 part as a distortion. Just my opinion. 

Sent from Yahoo Mail on Android 
 
  On Tue, 28 May 2019 at 13:48, Paul Emsley wrote:   
On 28/05/2019 11:51, Stephan Grunwald wrote:
> 
> I [have] recently solved [my] first X-ray structure and I would like to have 
> an opinion on 
> two questions, both dealing with secondary structure assignments.
>
> First of all, the wwPDBs says ”We encourage authors to use the calculated 
> helix (or sheet) records and not 
> provide their own remarks.” (https://www.wwpdb.org/documentation/procedure). 
> It says in the same 
> documentation, that the Promotif software will automatically assign SSE upon 
> deposition (does Promotif use 
> the DSSP algorithm?).

1) Your are encouraged, not mandated. ProMOTIF/dssp is one of a number of ways 
to generate secondary 
structure annotations. You seem to have a good reason to use "your own" 
assignment. Go ahead and do so, 
don't give it a second thought.

I don't have an opinion about question 2.

Paul.



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
  



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1

[ccp4bb] OFF topic Question Nucleotide exchange of RAS protein?

[Anamika Singh]

Hi All,

Does anyone know what is the actual difference between CIP and EDTA method
for exchanging the GppNHp (non-hydrolysable GTP) or GDP with the purified
RAS protein?

I have a protocol according to which I need to incubate the purified RAS
with GppNHp having 20U of alkaline phosphatase, 10uM of Zinc Chloride and
200mM ammonium sulfate for 2 hr at room temperature. In this protocol, they
have mentioned that ammonium sulfate needs to be added in the last. I am
quite confused, according to them do I need to add it after 2 hrs
incubation or I have to add this at last to the mixture of (purified
RAS+GppNHp+Zinc chloride and alkaline phosphatase)?

Since this protein and its mechanism is new to me so not sure what to do.
After reading some papers also I am not able to understand which method is
good for exchange and how these reactions behave?

Please help me in this regard.

-- 
Anamika Singh
Post-Doctoral Fellow
Silberman Institute of Life Sciences
Hebrew University of Jerusalem, Israel
No: 054-294-8036



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1

Re: [ccp4bb] Question on author provided HELIX/SHEET records and assignment of a continuous helix that changes its helix class.

[Paul Emsley]

On 28/05/2019 11:51, Stephan Grunwald wrote:


I [have] recently solved [my] first X-ray structure and I would like to have an opinion on 
two questions, both dealing with secondary structure assignments.


First of all, the wwPDBs says ”We encourage authors to use the calculated helix (or sheet) records and not 
provide their own remarks.” (https://www.wwpdb.org/documentation/procedure). It says in the same 
documentation, that the Promotif software will automatically assign SSE upon deposition (does Promotif use 
the DSSP algorithm?).


1) Your are encouraged, not mandated. ProMOTIF/dssp is one of a number of ways to generate secondary 
structure annotations. You seem to have a good reason to use "your own" assignment. Go ahead and do so, 
don't give it a second thought.


I don't have an opinion about question 2.

Paul.



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1

[ccp4bb] MX Support Scientist at Diamond Light Source

[david.h...@diamond.ac.uk]

Dear All

Closing date is approaching for this position – Sunday 2nd June

We are recruiting a senior support scientist to join the MX group at Diamond 
Light Source. The role involves developing and supporting the very active MX 
groups user programme, user support for our international user community, 
training and providing operational support to the group. Opportunities exist to 
work with us on developing automated systems for data collection and associated 
supporting infrastructure.

For further information please contact myself directly. For more details on the 
role and to apply please see:

https://vacancies.diamond.ac.uk/vacancy/mx-village-senior-support-scientist-383573.html

Best regards

Dave Hall
MX Science Group Leader
Diamond Light Source
www.diamond.ac.uk/mx




-- 
This e-mail and any attachments may contain confidential, copyright and or 
privileged material, and are for the use of the intended addressee only. If you 
are not the intended addressee or an authorised recipient of the addressee 
please notify us of receipt by returning the e-mail and do not use, copy, 
retain, distribute or disclose the information in or attached to the e-mail.
Any opinions expressed within this e-mail are those of the individual and not 
necessarily of Diamond Light Source Ltd. 
Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments 
are free from viruses and we cannot accept liability for any damage which you 
may sustain as a result of software viruses which may be transmitted in or with 
the message.
Diamond Light Source Limited (company no. 4375679). Registered in England and 
Wales with its registered office at Diamond House, Harwell Science and 
Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom




To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1

[ccp4bb] Postdoc vacancy in cryo-EM of Gene Regulatory Complexes at Schalch Lab, University of Leicester

[Schalch, Thomas (Dr.)]

Dear all,

A postdoctoral position is available in structural biology at the Leicester 
Institute of Structural and Chemical Biology, Department of Molecular and Cell 
Biology, University of Leicester.

We have an exciting opportunity for highly motivated postdoctoral candidates to 
lead a new project, which tackles fundamental questions in the regulation of 
gene expression through chromatin modification. The post of Research Associate 
is funded by the BBSRC to investigate the role of H2B ubiquitylation in 
heterochromatin formation and its mechanism in the promotion of euchromatic 
domains. The Research Associate will join a vibrant community at the University 
of Leicester's Department of Molecular and Cell Biology and will be based in 
the research group of Dr. Thomas Schalch, which has a long-standing interest in 
structural and functional understanding of chromatin and its impact on gene 
expression.

The Leicester Institute for Structural and Chemical Biology (LISCB) is a centre 
of research excellence initiated by the University of Leicester, which provides 
access to state-of-the-art integrated structural approaches comprising 
cryo-electron microscopy (Titan Krios G3), X-ray crystallography and 
biomolecular NMR.

For informal enquiries please contact Thomas Schalch directly by email at 
thomas.scha...@le.ac.uk.

Information on the application process and further details are available at 
https://jobs.le.ac.uk/vacancies/vacancy-details.aspx?VacancyID=1162.

--
Thomas Schalch, PhD
Associate Professor

Leicester Institute of Structural & Chemical Biology
Department of Molecular and Cell Biology
Henry Wellcome Building
University of Leicester
Lancaster Road, Leicester, LE1 7RH
United Kingdom

t: +44 116 229 7120
e: thomas.scha...@le.ac.uk
w: https://www.schalchlab.org




To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1