Re: [ccp4bb] interesting map problem

[Christine Gee]

Hi Eleanor,

I wonder if in fact this is the problem. I of course didn't think properly
about it. The cell is the same, sort of, and I think you have put your
finger on my error. It is the same data more or less, I was reprocessing a
dataset, to slightly higher resolution using the same images as for the
reference .mtz. The reference dataset was output from aimless (or whatever
package they used) with the default a
wrote:

> Well - that should not happen!
> Are the cell dimensions the same for the new data and the reference set?
> E
>
> On Fri, 17 Dec 2021 at 22:04, Christine Gee  wrote:
>
>> Hi,
>>
>> I recently came across this strange issue. I was using aimless in CCP4 to
>> scale my data and apply an Rfree from a reference .mtz
>>
>> Neither the reference or the file I was working with had higher
>> resolution than 1.5
>> However aimless wrote out h, k, l and Rfree to 0.4. I did not click the
>> button to extend resolution by the way.
>>
>> No big deal right? Well Coot then assumed the resolution was 0.4 and
>> wrote out maps to super high resolution and everything took forever to
>> render, making coot basically unuseable.
>>
>> I could not find any global or local parameter in coot that seemed to
>> remedy this.
>>
>> Did anyone come across anything similar? What is the solution besides
>> editing the resolution of the .mtz file output from aimless and what
>> program woud you recommend for this?
>>
>> My simple solution for now was to use an .mtz file output from aimless
>> that a reference Rfree was not applied to.
>>
>> Regards
>> Christine
>>
>>
>> --
>>
>> 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] interesting map problem

[Eleanor Dodson]

Christine - can you attach the relevant log files! Eleanor

On Fri, 17 Dec 2021 at 22:59, Ethan A Merritt  wrote:

> On Friday, 17 December 2021 14:04:17 PST Christine Gee wrote:
> > Hi,
> >
> > I recently came across this strange issue. I was using aimless in CCP4 to
> > scale my data and apply an Rfree from a reference .mtz
> >
> > Neither the reference or the file I was working with had higher
> resolution
> > than 1.5
> > However aimless wrote out h, k, l and Rfree to 0.4. I did not click the
> > button to extend resolution by the way.
> >
> > No big deal right? Well Coot then assumed the resolution was 0.4 and
> wrote
> > out maps to super high resolution and everything took forever to render,
> > making coot basically unuseable.
>
> Coot->File
> ->Open mtz
> select mtz file by name
> ->Expert Mode
> ->Use Resolution Limits
> set high resolution limit to 1.5
>
> However, I would worry that the spurious resolution is symptom of
> a more pervasive problem.
>
> Ethan
>
>
> >
> > I could not find any global or local parameter in coot that seemed to
> > remedy this.
> >
> > Did anyone come across anything similar? What is the solution besides
> > editing the resolution of the .mtz file output from aimless and what
> > program woud you recommend for this?
> >
> > My simple solution for now was to use an .mtz file output from aimless
> that
> > a reference Rfree was not applied to.
> >
> > Regards
> > Christine
> >
> > 
> >
> > To unsubscribe from the CCP4BB list, click the following link:
> > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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/
> >
>
>
> --
> Ethan A Merritt
> Biomolecular Structure Center,  K-428 Health Sciences Bldg
> MS 357742,   University of Washington, Seattle 98195-7742
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
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>
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> mailing list hosted by www.jiscmail.ac.uk, terms & conditions are
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Re: [ccp4bb] interesting map problem

[Ethan A Merritt]

On Friday, 17 December 2021 14:04:17 PST Christine Gee wrote:
> Hi,
> 
> I recently came across this strange issue. I was using aimless in CCP4 to
> scale my data and apply an Rfree from a reference .mtz
> 
> Neither the reference or the file I was working with had higher resolution
> than 1.5
> However aimless wrote out h, k, l and Rfree to 0.4. I did not click the
> button to extend resolution by the way.
> 
> No big deal right? Well Coot then assumed the resolution was 0.4 and wrote
> out maps to super high resolution and everything took forever to render,
> making coot basically unuseable.

Coot->File
->Open mtz
select mtz file by name
->Expert Mode
->Use Resolution Limits
set high resolution limit to 1.5

However, I would worry that the spurious resolution is symptom of
a more pervasive problem.

Ethan


> 
> I could not find any global or local parameter in coot that seemed to
> remedy this.
> 
> Did anyone come across anything similar? What is the solution besides
> editing the resolution of the .mtz file output from aimless and what
> program woud you recommend for this?
> 
> My simple solution for now was to use an .mtz file output from aimless that
> a reference Rfree was not applied to.
> 
> Regards
> Christine
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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/
> 


-- 
Ethan A Merritt
Biomolecular Structure Center,  K-428 Health Sciences Bldg
MS 357742,   University of Washington, Seattle 98195-7742



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Re: [ccp4bb] interesting map problem

[Eleanor Dodson]

Well - that should not happen!
Are the cell dimensions the same for the new data and the reference set?
E

On Fri, 17 Dec 2021 at 22:04, Christine Gee  wrote:

> Hi,
>
> I recently came across this strange issue. I was using aimless in CCP4 to
> scale my data and apply an Rfree from a reference .mtz
>
> Neither the reference or the file I was working with had higher resolution
> than 1.5
> However aimless wrote out h, k, l and Rfree to 0.4. I did not click the
> button to extend resolution by the way.
>
> No big deal right? Well Coot then assumed the resolution was 0.4 and wrote
> out maps to super high resolution and everything took forever to render,
> making coot basically unuseable.
>
> I could not find any global or local parameter in coot that seemed to
> remedy this.
>
> Did anyone come across anything similar? What is the solution besides
> editing the resolution of the .mtz file output from aimless and what
> program woud you recommend for this?
>
> My simple solution for now was to use an .mtz file output from aimless
> that a reference Rfree was not applied to.
>
> Regards
> Christine
>
>
> --
>
> 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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[ccp4bb] interesting map problem

[Christine Gee]

Hi,

I recently came across this strange issue. I was using aimless in CCP4 to
scale my data and apply an Rfree from a reference .mtz

Neither the reference or the file I was working with had higher resolution
than 1.5
However aimless wrote out h, k, l and Rfree to 0.4. I did not click the
button to extend resolution by the way.

No big deal right? Well Coot then assumed the resolution was 0.4 and wrote
out maps to super high resolution and everything took forever to render,
making coot basically unuseable.

I could not find any global or local parameter in coot that seemed to
remedy this.

Did anyone come across anything similar? What is the solution besides
editing the resolution of the .mtz file output from aimless and what
program woud you recommend for this?

My simple solution for now was to use an .mtz file output from aimless that
a reference Rfree was not applied to.

Regards
Christine



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[ccp4bb] EMBO Practical Course on High throughput protein production and crystallization, Marseille, July 2022

[Gerlind Sulzenbacher]

Dear colleagues,

I am glad to announce the "EMBO Practical Course on High throughput 
protein production and crystallization", hosted at the laboratory AFMB 
in Marseille, France, from 4 to 13 July 2022. On behalf of the 
organizers I would like to ask you to please let your colleagues and 
students know about our course by posting this information on the notice 
boards/webpage of your institute. Please feel free to download the 
course flyer for an A4 printout here:


https://meetings.embo.org/files/posters/21-protein-production.pdf

The course is intended for PhD students and young researchers using 
high-throughput methods for expression and crystallization of soluble 
proteins. The goal is to provide participants with the current knowledge 
in the use of the most innovative methods in the field.


Accommodation and subsistence are covered for accepted applicants.

For more information please visite the link below (in case of problems 
please copy the link into your browser)


https://meetings.embo.org/event/21-protein-production

Best wishes,
Gerlind, on behalf of the organizing committee

--
Gerlind Sulzenbacher
Architecture et Fonction des Macromolécules Biologiques
UMR7257 CNRS, Aix-Marseille Université
Case 932
163 Avenue de Luminy
13288 Marseille cedex 9
France
Tel +33 491 82 55 66
Fax +33 491 26 67 20
E-mail: gerlind.sulzenbac...@univ-amu.fr



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[ccp4bb] Structure Genomics Specialist for Protein Purification and Crystallization

[Karla J. F. Satchell]

The Center for Structural Genomics of Infectious Diseases at Northwestern 
University in Chicago has an immediate opening for a Research Technologist / 
Core Specialist.

This position is available to persons with a 4 year Bachelors degree and 2 
years experience in protein production and crystallization or with a Master’s 
degree and experience in this area.

Apply at

Core Tech
Northwestern University
Chicago, Illinois

https://careers.northwestern.edu/psp/hr857prd_er/EMPLOYEE/HRMS/c/HRS_HRAM_FL.HRS_CG_SEARCH_FL.GBL?Page=HRS_APP_JBPST_FL&Action=U&FOCUS=Applicant&SiteId=1&JobOpeningId=42861&PostingSeq=1


Note: Due to need to hire soon, this position in not compatible with persons 
who would need sponsorship for visas to work in the US.



Karla J. F. Satchell, Ph.D.
Anne Stewart Youmans Professor of Microbiology,
Northwestern University Feinberg School of Medicine
PI & Co-Director, Center for Structural Genomics of Infectious Diseases
Dept. of Microbiology-Immunology
303 E. Chicago Avenue, Ward 6-205
Chicago, IL 60611
312-503-2162
k-satch...@northwestern.edu








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smime.p7s
Description: S/MIME cryptographic signature

[ccp4bb] Beamline Scientist opening at Diamond Light Source

[Hall, Dave (DLSLtd,RAL,LSCI)]

Hi Everyone

We have an opening at Diamond for people interested in a beamline scientist 
role to join the team. More details can be found at:

https://vacancies.diamond.ac.uk/vacancy/macromolecular-crystallography-beamline-scientist-465689.html

The closing date for applications is Sunday 9th January.

Best wishes

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


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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 
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may sustain as a result of software viruses which may be transmitted in or with 
the message.
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Wales with its registered office at Diamond House, Harwell Science and 
Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom




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Re: [ccp4bb] the complex structure of protein and DNA

[Julia Griese]

Hi,

I agree with Mark, the R factors suggest that your model is more or less 
complete. It does not seem like that DNA is bound to your protein. Without 
knowing more about your project, it’s hard to make specific suggestions, but 
here goes:


  *   Have you actually checked that there is DNA in the complex crystals? 
(There can be other reasons why you have different cell parameters and space 
groups with and without DNA. It may just be different crystal forms. Were they 
crystallized in the same condition?) If not, wash the crystals, run them on a 
gel and stain for DNA.
  *   If you do have phosphate or sulphate in the crystallization condition, 
try to find a different condition without. It may well compete with DNA 
binding, since your affinity is low.
  *   Does the protein recognize a specific DNA sequence? If not, it may bind 
to different parts of the DNA molecule that you give it, and you will have lots 
of problems getting a complex crystal structure because you don’t have a 
uniform complex. The affinity you state being rather on the low side, I would 
suspect that this may be an issue.
  *   If you haven’t already, try different lengths of dsDNA. How much do you 
know about the footprint of the protein on DNA? How much do you know about the 
affinity of the protein for different DNA lengths? You need to find the sweet 
spot between affinity and length, i.e. the DNA should not be so short that it 
doesn’t bind well to the protein, but not so long that the complex won’t 
crystallize well because the DNA ends are floppy. You don’t say anything about 
the size of the protein, but 18 bp seems quite short to me, like that might be 
exactly the footprint of the protein on the DNA, but nothing more. Adding a few 
bp might help.
  *   This wouldn’t be my immediate next step since your problem seems to be 
that there isn’t any DNA in the crystals (at least not bound to the protein) in 
the first place, and you obviously need to solve that problem first, but using 
DNA with sticky ends can help to form crystal contacts and generate better 
crystals.
  *   Finally, are you sure about the space groups? Your R factors certainly 
suggest that you’re right, but P222 and P2 without any screw axes are very 
unusual. Also worth mentioning, although that doesn’t seem to be the issue 
here, is that DNA can cause pseudosymmetry that leads to space group 
misidentification, i.e. it looks like higher symmetry than it really is because 
the DNA is almost, but not really perfectly symmetrical. This can happen 
especially if you have a more or less palindromic DNA sequence, which is often 
the case with sequence-specific DNA-binding proteins.


Best,

Julia


--
Dr. Julia Griese
Assistant Professor
Department of Cell and Molecular Biology
Uppsala University
BMC, Box 596
SE-75124 Uppsala
Sweden

email: julia.gri...@icm.uu.se
phone: +46-(0)18-471 4982
http://www.icm.uu.se/structural-biology/griese-lab/

From: CCP4 bulletin board  on behalf of Mark Roe 

Reply-To: Mark Roe 
Date: Friday, 17 December 2021 at 12:16
To: "CCP4BB@JISCMAIL.AC.UK" 
Subject: Re: [ccp4bb] the complex structure of protein and DNA

Hi,

With this resolution and R-factors, I would guess you are not missing that much 
– certainly not large bits of DNA. Do you have Phosphate or Sulphate in the 
crystallisation buffer? If so, you may just be seeing Phosphate/Sulphate where 
the DNA would bind.

Cheers,
Mark


Dr S.M. Roe,
X-Ray Facility Manager, 
Tel. (+44) 01273 678863 (Office)
School of Life Sciences,
 Tel. (+44) 01273 872896 (X-Ray Lab)
University of Sussex,   
   Tel. (+44) 0782 5501579 (Mobile)
Falmer,
East Sussex.
 E-mail 
m@sussex.ac.uk
BN1 9RQ 
  Web   
http://www.sussex.ac.uk/lifesci/roelab/


From: CCP4 bulletin board  on behalf of Meiting Yang 

Reply to: Meiting Yang 
Date: Friday, 17 December 2021 at 08:04
To: "CCP4BB@JISCMAIL.AC.UK" 
Subject: Re: [ccp4bb] the complex structure of protein and DNA



Dear Petr,
Thank you very much for your reply!
The complex structure was refined finally to 2.44 Å resolution with an Rwork of 
23.7% and an Rfree of 27.4%.
We didn't try automatic DNA building tools, I don't know much about this. Thank 
you very much for your advice, I'm going to study it.
Could you please give some specific suggestions about automatic DNA building 
tools?
Thank you very much.











At 2021-12-17 15:01:44, "Petr Kolenko"  wrote:

>Dear Yang Meiting,

>There are few things to know better about your structures first:

>1) What is the reso

[ccp4bb] Available postdoctoral position in crystallography

[Apirat Chaikuad]

Hi all,

 

The Structural Genomics Consortium at the Goethe University Frankfurt offers
immediately a position of a Postdoctoral Scientist (m/f/d) limited initially
until 31st December 2023. Please see attached for job description.

 

We are looking for a motivated and experienced structural biochemist in the
field of protein crystallography for the development of allosteric
inhibitors.

 

You have a PhD in biology, chemistry biochemistry, biotechnology or similar.
You have profound knowledge in molecular biology and biochemistry and
experience in protein crystallography. Practical experience in biophysical
methods and experience of working abroad is a plus. You are comfortable to
work within an interdisciplinary team of international scientists with
different personalities and cultures. Fluency in English is a prerequisite.
You are passionate about your work and have a proactive attitude.

 

Application (CV and contact addresses of at least two referees in a single
PDF-file until 9th January 2022) or an informal enquiry should be made to
knapp(at)pharmchem.uni-frankfurt.de.

 

Best,

on behalf of Prof. Stefan Knapp

 




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Ausschreibung Knapp E13 TRABITA Xray Text english_extern.docx
Description: MS-Word 2007 document

Re: [ccp4bb] the complex structure of protein and DNA

[Mark Roe]

Hi,

With this resolution and R-factors, I would guess you are not missing that much 
– certainly not large bits of DNA. Do you have Phosphate or Sulphate in the 
crystallisation buffer? If so, you may just be seeing Phosphate/Sulphate where 
the DNA would bind.

Cheers,
Mark


Dr S.M. Roe,
X-Ray Facility Manager, 
Tel. (+44) 01273 678863 (Office)
School of Life Sciences,
 Tel. (+44) 01273 872896 (X-Ray Lab)
University of Sussex,   
   Tel. (+44) 0782 5501579 (Mobile)
Falmer,
East Sussex.
 E-mail 
m@sussex.ac.uk
BN1 9RQ 
  Web   
http://www.sussex.ac.uk/lifesci/roelab/


From: CCP4 bulletin board  on behalf of Meiting Yang 

Reply to: Meiting Yang 
Date: Friday, 17 December 2021 at 08:04
To: "CCP4BB@JISCMAIL.AC.UK" 
Subject: Re: [ccp4bb] the complex structure of protein and DNA



Dear Petr,
Thank you very much for your reply!
The complex structure was refined finally to 2.44 Å resolution with an Rwork of 
23.7% and an Rfree of 27.4%.
We didn't try automatic DNA building tools, I don't know much about this. Thank 
you very much for your advice, I'm going to study it.
Could you please give some specific suggestions about automatic DNA building 
tools?
Thank you very much.













At 2021-12-17 15:01:44, "Petr Kolenko"  wrote:

>Dear Yang Meiting,

>There are few things to know better about your structures first:

>1) What is the resolution of the complex structure?

>2) In what stage of structure refinement you are? Rwork/free would help.

>3) Have you tried some automatic DNA building tools?

>I am not surprised that you can see only a fraction of DNA.I guess, solvent 
>flattening may also decrease the visibility of this region. The only thing I 
>would suggest now, do not expect to see the whole DNA immediately. Just start 
>with the step-wise building if possible. The rest may appear in the later 
>stage of model building.

>Best regards,

>Petr

>

>From: CCP4 bulletin board  on behalf of Meiting Yang 
>

>Sent: Friday, December 17, 2021 7:29:54 AM

>To: CCP4BB@JISCMAIL.AC.UK

>Subject: [ccp4bb] the complex structure of protein and DNA

>

>Dear all，

>We have determined two Crystal structures, with one is apo structure and the 
>other is a complex of the same protein with double-stranded DNA. In the 
>complex, the protein structure is clearly viible, but the DNA only can be seen 
>several phosphate groups. We want to know how do we get the complete DNA 
>structure.

>The space group of the apo structure is P222, one asymmetric unit including 
>two protein molecules. The space group of the complex structure is P2, one 
>unit containing two protein molecules, 5 phosphate groups just situated near 
>one protein molecules. The binding ability of the DNA and the protein is about 
>1 μM. The DNA we used for crystallization is 18 bp double-stranded DNA, but 
>now only 5 phosphate groups can be observed. The crystal we have identified is 
>a complex rather than a monomer, the cell parameters of complexes and monomers 
>are different.

>Here, we want to get some suggestions, to get the complexe that contain the 
>entire DNA structure.

>Best regards.

>

>

>

>

>

>

>

>

>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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[ccp4bb] PhD and postdoc positions at Heidelberg University Biochemistry Center

[Klemens Wild]

*PhD and Postdoctoral Fellowship**s**- Structural biology**in 
***co-translational processes and **protein *homeostasis

*

Heidelberg University Biochemistry Center, University of Heidelberg, Germany

The group of Prof. Irmgard Sinningat the Heidelberg University 
Biochemistry Center(BZH) located in the picturesque Heidelberg of 
southwest Germany offers PhD and postdoctoral fellow/associate positions 
tohighly motivated scientists interested in tackling challenging 
questions in co-translational processes and protein homeostasis. We use 
an integrated approach of structural biology applying X-ray 
crystallography, single particle cryo-EM and complementary biophysical 
and biochemical techniques, and have constant access to the ESRF and 
state-of-the-art cryo-EM setup (Glacios and KRIOS/K3). We are part of an 
agile scientific community and have a long standing interestin 
unraveling detailed mechanismsof macromolecular machines from large 
protein/RNA complexes to membrane proteins. For details visit:


www.bzh.uni-heidelberg.de/sinning/ 



We are looking forward to your application including a CV, (degree) 
certificates, a list of publications, a letter of motivation and two 
letters of reference. Please send your application as single pdf 
document or ask for more information by email to: 
irmi.sinn...@bzh.uni-heidelberg.de 





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smime.p7s
Description: S/MIME Cryptographic Signature

[ccp4bb] Open position: Software and Controls Engineer at P11, DESY

[Hakanpää , Johanna]

Dear all,

We would like to draw your attention to an open position: Software and Controls 
Engineer, DESY, Hamburg.

DESY, with its more than 2700 employees at its two locations in Hamburg and 
Zeuthen, is one of the world's leading research centres for photon science, 
particle and astroparticle physics, and acceleration physics.

With the PETRA III storage ring and the free electron laser, DESY offers 
scientists and industrial customers a unique combination of photon sources. The 
High-throughput Macromolecular Crystallography beamline P11 offers high photon 
flux and a versatile experimental setup for the structure determination of 
crystalline biological samples. We are looking for a highly motivated software 
and controls engineer to strengthen our team.

For further information please see: 
https://v22.desy.de/e67416/records148667/index_eng.html

On behalf of the P11 team, Johanna


Johanna Hakanpää, PhD

Scientist, Beamline P11 (PETRA III)
Deutsches Elektronen-Synchrotron DESY
Notkestrasse 85
22607 Hamburg
Germany

Phone: +49 40 8998 5756
Email: johanna.hakan...@desy.de



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[ccp4bb] cryo-ET postdoc position in mitochondrial genome maintenance - Center for Protein Research at the University of Copenhagen

[Eva Kummer]

The newly established research group of Eva Kummer is looking for an excellent 
and highly motivated postdoc to investigate mitochondrial dynamics and their 
correlation with maintenance and expression of mitochondrial DNA. We look for 
someone to drive establishment of in situ imaging workflows including 
correlative light and electron microscopy, FIB milling and cryo-electron 
tomography. Prior experience with cryo-ET is therefore a big plus. This project 
will combine training and experimental work in house but also at other EM 
facilities in Europe and is the perfect project for someone with a big interest 
in method development and implementation.


Our group profits from generous funding by an NNF-CPR core grant and a Hallas 
Møller Emerging Investigator grant from the Novo Nordisk Foundation. We have 
access to state-of-the-art electron microscopy infrastructure at CFIM (Core 
Facility for Integrated Microscopy at the University of Copenhagen) including a 
Titan Krios and Glacios, both equipped with Falcon 3 DED. You will join an 
international and highly collaborative environment.


The position is available from May 2022 or as soon as possible thereafter.


For details, please visit: https://employment.ku.dk/faculty/?show=155424


Applications need to be submitted via the University online portal:

https://candidate.hr-manager.net/ApplicationForm/SinglePageApplicationForm.aspx?cid=1307&departmentId=19221&ProjectId=155424&MediaId=4636


For informal inquiries, please contact me directly: eva.kum...@cpr.ku.dk

https://www.cpr.ku.dk/research/protein-structure-function-program/kummer/


I am looking forward to your applications.

All the best,

Eva


Eva Kummer
Group Leader / Associate Professor

University of Copenhagen
Novo Nordisk Foundation Center for Protein Research
Protein Structure and Function Program
Blegdamsvej 3B
2200 København N


eva.kum...@cpr.ku.dk


https://www.cpr.ku.dk/research/protein-structure-function-program/kummer/

[1619797028382]


How
 we protect personal 
data





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Re: [ccp4bb] the complex structure of protein and DNA

[Meiting Yang]

Dear Petr,

Thank you very much for your reply!

The complex structure was refined finally to 2.44 Å resolution with an Rwork of 
23.7% and an Rfree of 27.4%.

We didn't try automatic DNA building tools, I don't know much about this. Thank 
you very much for your advice, I'm going to study it.

Could you please give some specific suggestions about automatic DNA building 
tools? 

Thank you very much.



















At 2021-12-17 15:01:44, "Petr Kolenko"  wrote:
>Dear Yang Meiting,
>There are few things to know better about your structures first:
>1) What is the resolution of the complex structure?
>2) In what stage of structure refinement you are? Rwork/free would help.
>3) Have you tried some automatic DNA building tools?
>I am not surprised that you can see only a fraction of DNA.I guess, solvent 
>flattening may also decrease the visibility of this region. The only thing I 
>would suggest now, do not expect to see the whole DNA immediately. Just start 
>with the step-wise building if possible. The rest may appear in the later 
>stage of model building.
>Best regards,
>Petr
>
>From: CCP4 bulletin board  on behalf of Meiting Yang 
>
>Sent: Friday, December 17, 2021 7:29:54 AM
>To: CCP4BB@JISCMAIL.AC.UK
>Subject: [ccp4bb] the complex structure of protein and DNA
>
>Dear all，
>We have determined two Crystal structures, with one is apo structure and the 
>other is a complex of the same protein with double-stranded DNA. In the 
>complex, the protein structure is clearly viible, but the DNA only can be seen 
>several phosphate groups. We want to know how do we get the complete DNA 
>structure.
>The space group of the apo structure is P222, one asymmetric unit including 
>two protein molecules. The space group of the complex structure is P2, one 
>unit containing two protein molecules, 5 phosphate groups just situated near 
>one protein molecules. The binding ability of the DNA and the protein is about 
>1 μM. The DNA we used for crystallization is 18 bp double-stranded DNA, but 
>now only 5 phosphate groups can be observed. The crystal we have identified is 
>a complex rather than a monomer, the cell parameters of complexes and monomers 
>are different.
>Here, we want to get some suggestions, to get the complexe that contain the 
>entire DNA structure.
>Best regards.
>
>
>
>
>
>
>
>
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>




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