[ccp4bb] Postdoctoral researcher at the Techical University of Denmark in structural biology

[Jens Preben Morth]

Postdoctoral researcher at the Technical University of Denmark
This position is offered in connection to the project Center for enzymatic 
deconstruction of thermoset plastics for a sustainable society (En’Zync). The 
center, which will start this coming fall and operate for at least six years, 
is made possible through the support of the Novo Nordisk Foundation. The center 
will offer excellent opportunities for further development of your carrier 
within biotechnology in general and enzyme technology in particular, and it 
houses leading expertise in the range of disciplines that are required for the 
discovery and -engineering industrial biocatalysts. Main center activities are 
within molecular biology, enzymology, structural biology, organic synthesis and 
computational biochemistry.
Responsibilities and qualifications
For the current position, we are seeking a postdoc, who can take a leading role 
in the organization and implementation of En`zync’s work at DTU. This includes 
direct participation in different research activities such enzyme screening, 
enzyme structural- and functional characterization and heterologous expression 
in fungal strains. In addition, we expect the post doc to participate in the 
supervision of younger students and the coordination of En`zync activities both 
internally at DTU and more broadly with researchers in the center located at 
Aarhus University, the Danish Technological Institute (DTI) and University of 
Porto.
To read more and apply for the position, please go to
https://efzu.fa.em2.oraclecloud.com/hcmUI/CandidateExperience/en/sites/CX_1/job/1064







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[ccp4bb] Postdoctoral researcher at the Techical University of Denmark

[Jens Preben Morth]

Postdoctoral researcher at the Technical University of Denmark
This position is offered in connection to the project Center for enzymatic 
deconstruction of thermoset plastics for a sustainable society (En’Zync). The 
center, which will start this coming fall and operate for at least six years, 
is made possible through the support of the Novo Nordisk Foundation. The center 
will offer excellent opportunities for further development of your carrier 
within biotechnology in general and enzyme technology in particular, and it 
houses leading expertise in the range of disciplines that are required for the 
discovery and -engineering industrial biocatalysts. Main center activities are 
within molecular biology, enzymology, structural biology, organic synthesis and 
computational biochemistry.
Responsibilities and qualifications
For the current position, we are seeking a postdoc, who can take a leading role 
in the organization and implementation of En`zync’s work at DTU. This includes 
direct participation in different research activities such enzyme screening, 
enzyme structural- and functional characterization and heterologous expression 
in fungal strains. In addition, we expect the post doc to participate in the 
supervision of younger students and the coordination of En`zync activities both 
internally at DTU and more broadly with researchers in the center located at 
Aarhus University, the Danish Technological Institute (DTI) and University of 
Porto.
To read more and apply for the position, please go to
https://www.dtu.dk/english/about/job-and-career/vacant-positions/job?id=cfb6eda2-09ca-4ca8-be5e-5790fa35d415




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[ccp4bb] Memrbane Structural Biology and characterization position at the Technical University of Denmark

[Jens Preben Morth]

Dear Colleagues,

There is an opening for a post doc position at the Technical University in 
Denmark
Check out this link for more information
https://www.dtu.dk/om-dtu/job-og-karriere/ledige-stillinger/job?id=df8299c8-5e73-4e7b-94c4-f4e3a0ba80d5

Best Preben

Best regards

J. Preben Morth

Professor


DTU Bioengineering



Technical University of Denmark

Department of Biotechnology and Biomedicine

Søltofts Plads

Building 224, Room 128

2800 Kgs. Lyngby

pr...@dtu.dk

www.dtu.dk/english












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Re: [ccp4bb] Job posting: Post doc at the Technical University in Denmark, within Ubiquitin signalling.

[Jens Preben Morth]

With link
Dear ccp4bb
I wish to draw your attention to a job opportunity at my colleague's laboratory 
here at the Danish Technical University. Rune Busk Damsgaard is looking for a 
protein engineer to join his laboratory to work on an exciting project within 
Ubiquitin signalling.
Follow the link below to apply
https://www.bioengineering.dtu.dk/english/about/jobliste/job?id=5e88f8b3-b2b4-4d82-9bd8-ac7c25c05c22

best Preben


From: Jens Preben Morth 
Date: Thursday, 29 July 2021 at 11:13
To: "CCP4BB@JISCMAIL.AC.UK" 
Subject: [ccp4bb]Job posting: Post doc at the Technical University in Denmark, 
within Ubiquitin signalling.

Dear ccp4bb
I wish to draw your attention to a job opportunity at my colleague's laboratory 
here at the Danish Technical University. Rune Busk Damsgaard is looking for a 
protein engineer to join his laboratory to work on an exciting project within 
Ubiquitin signalling.
Follow the link below to apply




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[ccp4bb] Job posting: Post doc at the Technical University in Denmark, within Ubiquitin signalling.

[Jens Preben Morth]

Dear ccp4bb
I wish to draw your attention to a job opportunity at my colleague's laboratory 
here at the Danish Technical University. Rune Busk Damsgaard is looking for a 
protein engineer to join his laboratory to work on an exciting project within 
Ubiquitin signalling.
Follow the link below to apply




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

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
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[ccp4bb] PhD position at Oslo University

[Jens Preben Morth]

Dear CCP4,

Could you please forward the following position to suitable candidates.

Application must go through the following website, the closing date is 
the 9th of January.


https://uio.easycruit.com/vacancy/preview/4652201a9d62f4804df76cde9facf361/1753239/70932

best regards Preben

Centre for Molecular Medicine Norway (NCMM)
PhD Candidate in membrane protein chemistry

*Background:*

A 3-year PhD position is available in the laboratory of Dr. Preben 
Morth. The position is funded by Norforsk (https://www.nordforsk.org/en) 
and is a collaboration between Oslo, Lund and Copenhagen university. The 
student will be expected to travel to either Lund or Copenhagen as part 
of this study. The aim is to understand how the lipid environment 
influences the activity of membrane proteins, using the active 
transporter MgtA as benchmark system, and to investigate the dynamic 
fluctuations between lipid and protein in solution.


**

*The  candidate:*

We search for highly motivated individuals to work in the field of 
membrane protein chemistry. The ideal candidate have previous experience 
in membrane protein expression and purification for structural analysis 
as well as experience with enzyme kinetics and the use of small angle 
X-ray scattering (SAXS) or small angle neutron scattering (SANS). 
Applicants with knowledge on membrane protein characterization using 
biophysical methods will be prioritized. The candidate should be 
self-motivated, have excellent interpersonal, communication skills and a 
demonstrated ability to interact effectively with staff at all levels 
within a multi-disciplinary team.


*The application:*

**The application should include:

1. A one-page statement of motivation and research interests
2. CV
3. Names and contact details of 2-3 references (name, relation to
   candidate, e-mail and telephone number)

Re: [ccp4bb] Blob Game

[jens Preben Morth]

a horrible water molecule would fit in there :-)

On 23/02/15 19:42, Keller, Jacob wrote:

A little more info:

-Resolution is 1.75 Ang at edge of detector, but I/sig was still ~3; pushing 
integration to corners gives 1.66 Ang, but completeness is horrible. The home 
setup was at the limit (without 2 theta.)

-Data are horribly twinned with fractions of 58/42%, spacegroup is P3212. 
Besides that, though, the data are really excellent.

-Peak is 6.40 rmsd in Refmac-generated difference map.

-Distance from blob-peak to Arg-N is 3.43 Ang, but the peak is obviously not 
spherical.

JPK



-Original Message-
From: Keller, Jacob
Sent: Monday, February 23, 2015 12:34 PM
To: Keller, Jacob; CCP4BB@JISCMAIL.AC.UK
Subject: RE: Blob Game

...And the cryoprotectant was simply the Li/NH4SO4 mother liquor. Also maybe 
relevant: the crystals were pretty old, a year or so.

JPK

-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Keller, 
Jacob
Sent: Monday, February 23, 2015 12:21 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Blob Game

Dear Crystallographers,

I've got a strange blob hanging off an arginine--see attached. Any ideas? 
Nothing weird in the prep; cryst+prot conditions: NH4SO4, TRIS/HEPES, CaCl2, 
NaCl, Li2SO4. There are really no other side chains which could be close 
enough, and there's nothing in the anomalous LLG map.

???

JPK

***
Jacob Pearson Keller, PhD
Looger Lab/HHMI Janelia Research Campus
19700 Helix Dr, Ashburn, VA 20147
email: kell...@janelia.hhmi.org
***


--
J. Preben Morth, Ph.D
Group Leader
Membrane Transport Group
Nordic EMBL Partnership
Centre for Molecular Medicine Norway (NCMM)
University of Oslo
P.O.Box 1137 Blindern
0318 Oslo, Norway
Tel: +47 2284 0794

Re: [ccp4bb] Two Postdoc positions, one in cellular immunology/cell biology and one in structural biology.

[jens Preben Morth]

Sorry for the double posting, but the previous link to the position does 
not have the right link

please follow the link below for application
http://uio.easycruit.com/vacancy/1253461/96323?iso=no
best Preben

On 08/09/14 10:55, jens Preben Morth wrote:

Dear CCP4 members
Could you please forward the following to suitable candidates.
The position will soon be available from the following website
http://www.uio.no/om/jobb/ledige-stillinger/#vrtx-main-content-2
Best Preben

*Department of Biosciences/Centre for Molecular Medicine (NCMM), 
Nordic EMBL Partnership, University of Oslo.***


Two 2-year positions as researcher are available at the NRC project 
The intracellular pathway for MHC Class II antigen presentation. One 
of the positions will work in the group of prof. Oddmund Bakke at the 
Department of Biosciences and the second in the group of Dr. Preben 
Morth at the Centre for Molecular Medicine, University of Oslo. A one 
year prolongation is possible.


*Job Description*

The project focuses primarily on unraveling the function of the 
endocytic pathway toward antigen loading using biophysical techniques, 
molecular biological techniques, protein crystallography, 
biochemistry, imaging (e.g live imaging) and 
molecular/imaging/biochemical screens in cell culture systems and 
cells from knock out/knock in mice. The project will focus on 
unraveling the pathway toward MHC II antigen loading, in particular 
the molecules associate with the transport to and from this 
compartment in immune cells(See e.g. Neefjes et al., 2011, Nature 
immunology ihttp://www.ncbi.nlm.nih.gov/pubmed/22076556). The Morth 
Group is a part of the Centre for Molecular Medicine Norway, home 
page: http://www.ncmm.uio.no/research/groups/membrane-transport/. The 
Bakke group is a member of a CoE,Centre for Immune Regulation 
http://www.med.uio.no/cir/english/and prof Oddmund Bakke is also the 
head of the National imaging platform NorMIC 
Oslo,http://www.mn.uio.no/ibv/english/research/about/infrastructure/imaging/


with a wide range of imaging equipment. The work will include 
collaboration with national and international groups in particular 
Prof. Jacques Neefjes at the Dutch Cancer Centre, NKI in Amsterdam. 
http://www.nki.nl/divisions/cell-biology-ii/neefjes-s-group/.


We are seeking highly motivated and skilled researchers with broad and 
extensive experience within one or more of the following areas: 
advanced imaging, molecular biology, cellular immunology, cell 
biology, biochemistry, protein chemistry. Prior experience with 
intracellular membrane/protein traffic and library screening will be 
considered a strong advantage. One of the positions will 
preferentially have experience withprotein crystallography and/or 
biophysical methods.


*Qualifications:*

The Faculty of Mathematics and Natural Sciences has a strategic 
ambition of being a leading research faculty. Candidates for these 
fellowships will be selected in accordance with this, and expected to 
be in the upper segment of their class with respect to academic 
credentials.


The candidates must have a PhD or other corresponding education 
equivalent to a Norwegian doctoral degree in molecular biology, cell 
biology, biophysics or biochemistry or structural biology.


A good command of English is required.

English proficiency requirements 
http://www.mn.uio.no/english/research/doctoral-degree-and-career/regulations/proficiency-requirements.html


*The application must include:*

.Application letter

.CV (summarizing education, positions, research experience and other 
qualifying activity)


.Copies of educational certificates, letters of recommendation, and a 
list of reference persons


.A complete list of publications and all academic work that the 
applicant wishes to be considered by the evaluation committee


.Names and contact details of 2-3 references (name, relation to 
candidate, email address, and telephone number)


Please remember that *all* documents should be in English or a 
Scandinavian language.


The University of Oslo has an agreement for all employees, aiming to 
secure rights to research results a.o.


In accordance with the University of Oslo's equal opportunities 
policy, we invite applications from all interested individuals 
regardless of gender or ethnicity.


--
J. Preben Morth, Ph.D
Group Leader
Membrane Transport Group
Nordic EMBL Partnership
Centre for Molecular Medicine Norway (NCMM)
University of Oslo
P.O.Box 1137 Blindern
0318 Oslo, Norway
Tel: +47 2284 0794




--
J. Preben Morth, Ph.D
Group Leader
Membrane Transport Group
Nordic EMBL Partnership
Centre for Molecular Medicine Norway (NCMM)
University of Oslo
P.O.Box 1137 Blindern
0318 Oslo, Norway
Tel: +47 2284 0794

[ccp4bb] Two Postdoc positions, one in cellular immunology/cell biology and one in structural biology.

[jens Preben Morth]

Dear CCP4 members
Could you please forward the following to suitable candidates.
The position will soon be available from the following website

http://www.uio.no/om/jobb/ledige-stillinger/#vrtx-main-content-2

Best Preben

*Department of Biosciences/Centre for Molecular Medicine (NCMM), 
Nordic EMBL Partnership, University of Oslo.***


Two 2-year positions as researcher are available at the NRC project The 
intracellular pathway for MHC Class II antigen presentation. One of the 
positions will work in the group of prof. Oddmund Bakke at the 
Department of Biosciences and the second in the group of Dr. Preben 
Morth at the Centre for Molecular Medicine, University of Oslo. A one 
year prolongation is possible.


*Job Description*

The project focuses primarily on unraveling the function of the 
endocytic pathway toward antigen loading using biophysical techniques, 
molecular biological techniques, protein crystallography, biochemistry, 
imaging (e.g live imaging) and molecular/imaging/biochemical screens in 
cell culture systems and cells from knock out/knock in mice. The project 
will focus on unraveling the pathway toward MHC II antigen loading, in 
particular the molecules associate with the transport to and from this 
compartment in immune cells(See e.g. Neefjes et al., 2011, Nature 
immunology ihttp://www.ncbi.nlm.nih.gov/pubmed/22076556). The Morth 
Group is a part of the Centre for Molecular Medicine Norway, home page: 
http://www.ncmm.uio.no/research/groups/membrane-transport/. The Bakke 
group is a member of a CoE,Centre for Immune Regulation 
http://www.med.uio.no/cir/english/and prof Oddmund Bakke is also the 
head of the National imaging platform NorMIC 
Oslo,http://www.mn.uio.no/ibv/english/research/about/infrastructure/imaging/


with a wide range of imaging equipment. The work will include 
collaboration with national and international groups in particular Prof. 
Jacques Neefjes at the Dutch Cancer Centre, NKI in Amsterdam. 
http://www.nki.nl/divisions/cell-biology-ii/neefjes-s-group/.


We are seeking highly motivated and skilled researchers with broad and 
extensive experience within one or more of the following areas: advanced 
imaging, molecular biology, cellular immunology, cell biology, 
biochemistry, protein chemistry. Prior experience with intracellular 
membrane/protein traffic and library screening will be considered a 
strong advantage. One of the positions will preferentially have 
experience withprotein crystallography and/or biophysical methods.


*Qualifications:*

The Faculty of Mathematics and Natural Sciences has a strategic ambition 
of being a leading research faculty. Candidates for these fellowships 
will be selected in accordance with this, and expected to be in the 
upper segment of their class with respect to academic credentials.


The candidates must have a PhD or other corresponding education 
equivalent to a Norwegian doctoral degree in molecular biology, cell 
biology, biophysics or biochemistry or structural biology.


A good command of English is required.

English proficiency requirements 
http://www.mn.uio.no/english/research/doctoral-degree-and-career/regulations/proficiency-requirements.html


*The application must include:*

.Application letter

.CV (summarizing education, positions, research experience and other 
qualifying activity)


.Copies of educational certificates, letters of recommendation, and a 
list of reference persons


.A complete list of publications and all academic work that the 
applicant wishes to be considered by the evaluation committee


.Names and contact details of 2-3 references (name, relation to 
candidate, email address, and telephone number)


Please remember that *all* documents should be in English or a 
Scandinavian language.


The University of Oslo has an agreement for all employees, aiming to 
secure rights to research results a.o.


In accordance with the University of Oslo's equal opportunities policy, 
we invite applications from all interested individuals regardless of 
gender or ethnicity.


--
J. Preben Morth, Ph.D
Group Leader
Membrane Transport Group
Nordic EMBL Partnership
Centre for Molecular Medicine Norway (NCMM)
University of Oslo
P.O.Box 1137 Blindern
0318 Oslo, Norway
Tel: +47 2284 0794

[ccp4bb] position lab manager

[jens Preben Morth]

Dear Colleagues
Please forward this to suited candidates, candidates must apply through 
the link, sorry for the Norwegian (Scandinavian'ish) requirement, the 
candidate needs to be able to navigate around in the purchase portal 
only offered in Norwegian.

http://uio.easycruit.com/vacancy/1225339/70932?iso=no
best regards
Preben

Centre for Molecular Medicine Norway (NCMM)
Laboratory Manager/Principal Engineer

The one-year position, with possibilities for extension to 3 more years, 
is available in the laboratory of Dr. J. Preben Morth from 15th of August.


*Challenges:*

The group is interested on the systems involved with pH homeostasis. The 
main techniques used are cloning, expression purification and 
crystallization. The position will also include work with mammalian 
cells and various imaging techniques.  The lab manager will play an 
active role in laboratory research projects and maintaining group resources.


*Laboratory tasks include:*

 * Cloning including primer design PCR reaction, subcloning in both
   bacterial and cell lines
 * Protein purification of both soluble and membrane proteins
 * Cell line transfection
 * Crystallisation, computer support.
 * Maintaining the laboratory self made resources such as competent cells.

*Qualifications:*

 * Formal requirement with regard to education is a masters degree in
   biochemistry /molecular biology as minimum however a PhD would be
   preferred. Experience from similar work can replace this formal
   requirement.
 * Experience with protein chemistry, protein crystallography and
   biophysical methods is preferred
 * Work knowledge of Word and Excel
 * The candidate must have basic knowledge in Norwegian, both written
   and oral
 * The group has a number of international collaborations and the
   position requires applicants to be highly organized and fluent in
   English
 * Open and friendly nature, not afraid to learn something new


--
J. Preben Morth, Ph.D
Group Leader
Membrane Transport Group
Nordic EMBL Partnership
Centre for Molecular Medicine Norway (NCMM)
University of Oslo
P.O.Box 1137 Blindern
0318 Oslo, Norway
Tel: +47 2284 0794

Re: [ccp4bb] Fwd: Akta Service

[jens Preben Morth]

  
  
Dear James 
There is no excuse for this intrusion, please refrain from making
this another digital goat marked.
cheers
Preben
On 3/4/14 2:51 PM, James Bull wrote:


  
  
  

 Original Message 

  

  Subject:

  
  Akta Service


  Date:
  
  Tue, 04 Mar 2014 10:44:09 +


  From:
  
  sa...@holmesanalytical.co.uk


  To: 
  CCP4BB@JISCMAIL.AC.UK

  




Dear Sirs, please excuse our intrusion - 

During our search for Akta users within the UK we have come
across your details and specifically the subject of service
provisions on FPLC instruments.

We at Holmes Analytical are a company who specialise in the
service of these instruments and support many customers in the
UK including the MIB in Manchester, Syngenta and Cancer
Research.

If you would like to know more about our company, please just
ask - again, apologies for the intrusion

Kind regards

James

James Bull
  
  

Mobile:07429 592254
Office:0044 845 430 8466
Fax:0044 1233 221600

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www.holmesanalytical.co.uk
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kindly note that email communications are not secured and
therefore are susceptible to alteration. Holmes Analytical
Limited will not accept legal responsibility for the
contents of this message. If you have received this message
in error please advise the sender by reply email, and delete
the message. Thank you for your co-operation.



  
  


-- 
J. Preben Morth, Ph.D
Group Leader
Membrane Transport Group
Nordic EMBL Partnership
Centre for Molecular Medicine Norway (NCMM)
University of Oslo
P.O.Box 1137 Blindern
0318 Oslo, Norway
Tel: +47 2284 0794



  

[ccp4bb] Position in Chemical and systems biology in Oslo

[jens Preben Morth]

Dear CCP4bb
please forward to candidates that might be interested
http://uio.easycruit.com/vacancy/1125923/70931?iso=gb
best Preben

--
J. Preben Morth, Ph.D
Group Leader
Membrane Transport Group
Nordic EMBL Partnership
Centre for Molecular Medicine Norway (NCMM)
University of Oslo
P.O.Box 1137 Blindern
0318 Oslo, Norway
Tel: +47 2284 0794

Re: [ccp4bb] Best compounds for heavy atom soaks

[jens Preben Morth]

Hi
do not forget the clusters like Ta6Br12 or the lanthanides.
in case your interesting protein is a membrane protein there are some 
choices that might work better than other

we have described it here.
http://www.ncbi.nlm.nih.gov/pubmed/16855303
This is not exclusive to membrane proteins at all. My personal favorite 
is orange platinum, with an acupunture needle stick the tip in the 
orange platinum powder, and and gently let the needle hoover over the 
drop, the static electricity will pull some orange platinum crystals 
into your drop without disturbing it. This is really nice if you have 
mechanically sensitive crystals. Then just seal the drop and wait for 
the orange color to emerge. Its almost like cooking a restaurant dish, 
just more expensive.

cheers
Preben

On 1/15/14 6:18 PM, RHYS GRINTER wrote:

Hello message board,

My group has some crystals of an interesting protein to take to the synchrotron 
in a couple of weeks. We won't be able to prepare and crystallise a SelMet 
derivative during that time period, but we have loads of crystals sitting 
around. The diffraction isn't great, we see maybe 3.5 at home but might be 
enough to get over the line.
It will be a very difficult MR target, so we were thinking of soaking so 
crystals with heavy atomic compounds that we have lying around. I was wondering 
if people had any suggestions of compounds that people have used successfully 
for experimental phasing and maybe concentrations to use and soaking time.

Cheers,

Rhys


--
J. Preben Morth, Ph.D
Group Leader
Membrane Transport Group
Nordic EMBL Partnership
Centre for Molecular Medicine Norway (NCMM)
University of Oslo
P.O.Box 1137 Blindern
0318 Oslo, Norway
Tel: +47 2284 0794

Re: [ccp4bb] Can not optimize

[jens Preben Morth]

Hi Omi
Did you test them for diffraction? you might want to keep screening 
broad for better crystals.  You could try to add K/NaSCN, KI or KNO3 as 
an additive (50 mM) to you protein mix and go from there

best Preben
On 8/23/13 4:56 AM, zhuqing ouyang wrote:
Dear all, I am trying to crystallize a protein complex, the initial 
screening result shows that several hints look like microcrystals. see 
pictures attached. The conditions are very similar:

1. 0.2 M NaI, 20% 3350
2. 0.2 M KI, 20% 3350
3. 0.2 M NaSCN, 20% 3350
4. 0.2 M KSCN, 20% 3350
5. 0.2 M NaNO3, 20% 3350
6. 0.2 M KNO3, 20% 3350

But I can not get bigger crystals around those conditions. Any 
comments or suggestions would be appreciated.

best
omi



--
J. Preben Morth, Ph.D
Group Leader
Membrane Transport Group
Nordic EMBL Partnership
Centre for Molecular Medicine Norway (NCMM)
University of Oslo
P.O.Box 1137 Blindern
0318 Oslo, Norway

Email: j.p.mo...@ncmm.uio.no
Tel: +47 2284 0794

http://www.jpmorth.dk

Re: [ccp4bb] Calcium ions in enzymes

[jens Preben Morth]

Hi Wei
The sarco(endo)plasmic reticulum Calcium ATPase (SERCA) require Calcium 
as a substrate to be functional.

Preben
On 5/31/13 12:25 PM, Wei Liu wrote:

Dear all,

As we all know, many proteins contain calcium ions. Does anyone know if there 
are reported cases where calcium ions play a catalytic role rather than a 
structural role in enzymes?

Best
Wei Liu


--
J. Preben Morth, Ph.D
Group Leader
Membrane Transport Group
Nordic EMBL Partnership
Centre for Molecular Medicine Norway (NCMM)
University of Oslo
P.O.Box 1137 Blindern
0318 Oslo, Norway

Email: j.p.mo...@ncmm.uio.no
Tel: +47 2284 0794

http://www.jpmorth.dk

Re: [ccp4bb] Organic solvents for ligand solubilisation

[jens Preben Morth]

Dear Klaus
If your compound can be dried, you can add it to the drop as a powder 
from the tip of a acupuncture needle. At least this works for many of 
the insoluble heavy metal derivatives. We have also successfully 
resuspended the powder in the optimal buffer of choice and added it as 
insoluble power in solution.

cheers
Preben
On 5/23/13 3:36 PM, Klaus Fütterer wrote:

Dear CCP4BB followers,

We are currently trying to obtain ligand-bound complexes for one of 
our proteins by soaking and/or co-crystallisation. We have had prior 
success for this protein, but using  a different class of ligands. The 
new ligand (in DMSO) remains in solution (more or less) when mixed 
with the reservoir/cryoprotectant, and the diffraction pattern 
survives the soaking nicely. Annoyingly though,  all we see are 
density peaks that match the size of DMSO and become more pronounced 
when increasing [DMSO] (to help solubilisation of the ligand). Soaking 
times varied between minutes to 16 hours. Kd was measured ( ~ 10 uM) 
in the solution state.


We have tried pyridine (which keeps the ligand in solution, but kills 
diffraction in an instant), and DMF (which doesn't keep the ligand in 
solution when mixing with cryoprotectant).


I am wondering whether the community has suggestions for alternative 
organic solvents that have been used to solubilise hydrophobic 
ligands, and are reasonably gentle to the protein crystal.


Thank you.

Klaus


===

Klaus Fütterer, Ph.D.
Reader in Structural Biology
  Undergraduate Admissions

School of Biosciences  P: +44-(0)-121-414 5895
University of Birmingham  F: +44-(0)-121-414 5925
Edgbaston E: k.futte...@bham.ac.uk 
mailto:k.futte...@bham.ac.uk

Birmingham, B15 2TT, UK   W: http://tinyurl.com/futterer-lab
===







--
J. Preben Morth, Ph.D
Group Leader
Membrane Transport Group
Nordic EMBL Partnership
Centre for Molecular Medicine Norway (NCMM)
University of Oslo
P.O.Box 1137 Blindern
0318 Oslo, Norway

Email: j.p.mo...@ncmm.uio.no
Tel: +47 2284 0794

http://www.jpmorth.dk

Re: [ccp4bb] protein degradation in crystal

[jens Preben Morth]

Dear Lisa
It is not uncommon to see breakdown products when you run crystals on  
gel. Espesially if they are older crystals, sometimes you even see 
higher molecular bands, these are probably due to intra molecular cross 
links formed over time.
If you are worried about stability, try to increase the crystallization 
speed, we have one example where we see a clear difference in both 
crystal quality and even space group depending on when we fish the 
crystals. The crystals appear within 5 min,  the best quality data sets 
come from crystals  we fish after only 30-60 min.
You may also have a little protease contamination of course, to prevent 
this add protease inhibitor, or DTT, or EDTA to you protein before you 
set it up.

cheers Preben

On 1/16/13 12:14 PM, LISA wrote:

Hi All,
I have an 36KD protein which can be crystallize in two days. Most of 
the crystals are very big. But all cystals have poor resolution,lower 
than 3.8 A. I picked some crystals, washed them in the mother solution 
and then run SDS-PAGE. It is surprised to find that different cystals 
have different components. Some crystals have several samll bands 
below the band of the protein. And in some crysals the bigger size 
band (as the construct should be) almost disappared and have smear. 
Does the protein was degradated in the crystals? Did someone met the 
similar problem as I? Thanks


All the best
lisa


--
J. Preben Morth, Ph.D
Group Leader
Membrane Transport Group
Nordic EMBL Partnership
Centre for Molecular Medicine Norway (NCMM)
University of Oslo
P.O.Box 1137 Blindern
0318 Oslo, Norway

Email: j.p.mo...@ncmm.uio.no
Tel: +47 2284 0794

http://www.jpmorth.dk

Re: [ccp4bb] a challenge

[jens Preben Morth]

I agree with Tassos, and btw think that this crystallographer, should be 
able to go back into the lab and optimize the present crystal conditions 
to get better crystals. In particularly, when he or she realize that the 
scientific question they set out to investigate cannot be answered, by 
analyzing the final structure, with the available data quality.

Preben


On 1/13/13 8:52 PM, Anastassis Perrakis wrote:

I think the real challenge (and one that makes for an excellent macromolecular 
crystallographer) is how well one can interpret a map with poor phases.

Let me disagree ... An excellent macromolecular crystallographer, is one that 
given some crystals can derive the best strategy to collect data,
process the data optimally, derive phases using all available information, 
build a model and refine it in such a way that it best explains both data
and geometrical expectations, and do these as efficiently as possible.

Efficiency may suggest using one automated suite or another - or indeed may 
best be achieved by manual labor - be it in the map or in data
collection strategy or refinement or another step: and here I am ignoring the 
art of transforming hair-needle-crystalline-like-dingbits to a diffracting 
crystal.

One that can interpret a map with poor phases can be either a genius in 3d 
orientation - or a not necessarily too intelligent nor experienced but 
determined student
that can drink and breathe this map for a few weeks in a row until a solution 
is in place. Neither would make an excellent macromolecular crystallographer by 
necessity.

Tassos

Re: [ccp4bb] Serine

[jens Preben Morth]

Dear Uma

1. The protein sequence given in the databases, do from time to time 
have errors,  particularly if you are working with old proteins (when 
the sequencing was done a long time ago). What you observe could also be 
a threonine or even a valine. You should check whether homologous 
protein also have a serine on that position.  I Normally do not assign 
double conformation unless you have fairly high resolution data, it is a 
bit hard to judge what the resolution is here. Often a double 
conformation is accompanied with negative difference density on top of 
the assigned atom, if you lower the sigma level  a little, you often see it.


2. It is also common to have local frameshift errors in loop regions, 
even in reasonable high resolution data. I think you should double check 
the region to make sure you are not facing this problem, it is 
surprisingly difficult to detect sometimes, but you will know when you 
got the right.


Cheers
Preben

On 5/21/12 10:57 PM, Uma Ratu wrote:

Dear All:
Some of serine residues in my model have extra positive Fo-Fc density 
at the edge of side chain. Some don't have. It is not like from 
phosphates.
I am wondered what is the cause for these extra density. Could these 
serines be post-translational modified?
I have the images attached. P289ser-0512-1 does not have the extra 
green, where P140ser-0512-1 has.

Thank you for you advice and comment
Uma


--
J. Preben Morth, Ph.D
Group Leader
Membrane Transport Group
Nordic EMBL Partnership
Centre for Molecular Medicine Norway (NCMM)
University of Oslo
P.O.Box 1137 Blindern
0318 Oslo, Norway

Email: j.p.mo...@ncmm.uio.no
Tel: +47 2284 0794

http://www.jpmorth.dk

Re: [ccp4bb] Serine

[jens Preben Morth]

3. Of course if you are working on recombinant protein, you should 
double check the sequencing results from the cloning

Preben

On 5/21/12 11:21 PM, Uma Ratu wrote:

Thank you All for you inputs.
Uma

On Mon, May 21, 2012 at 5:06 PM, Van Den Berg, Bert 
lambertus.vandenb...@umassmed.edu 
mailto:lambertus.vandenb...@umassmed.edu wrote:


Yes, as Jacob says, alternative conformation of the serine. Quite
common.

Bert

*From:* CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK
mailto:CCP4BB@JISCMAIL.AC.UK] on behalf of Uma Ratu
[rosiso2...@gmail.com mailto:rosiso2...@gmail.com]
*Sent:* Monday, May 21, 2012 4:57 PM

*To:* CCP4BB@JISCMAIL.AC.UK mailto:CCP4BB@JISCMAIL.AC.UK
*Subject:* [ccp4bb] Serine

Dear All:
Some of serine residues in my model have extra positive Fo-Fc
density at the edge of side chain. Some don't have. It is not like
from phosphates.
I am wondered what is the cause for these extra density. Could
these serines be post-translational modified?
I have the images attached. P289ser-0512-1 does not have the extra
green, where P140ser-0512-1 has.
Thank you for you advice and comment
Uma




--
J. Preben Morth, Ph.D
Group Leader
Membrane Transport Group
Nordic EMBL Partnership
Centre for Molecular Medicine Norway (NCMM)
University of Oslo
P.O.Box 1137 Blindern
0318 Oslo, Norway

Email: j.p.mo...@ncmm.uio.no
Tel: +47 2284 0794

http://www.jpmorth.dk

Re: [ccp4bb] Real Space Refine Zone for Ligand

[jens Preben Morth]

Hi Dipankar
you need to pit a unique identifier for each of your ligands,
eg
phenix.elbow --smiles=cyclopiazonic_acid.smi --id=CZA --output=cza --opt

best Preben

On 4/16/12 4:52 AM, Dipankar Manna wrote:


Dear Crystallographers,

After one round of refinement (restrained refinement) with ligand, I 
inport the .cif file through '-Import CIF Dictionary' into Coot. But 
when I am going for '-Real Space Refine Zone' for the ligand, its 
showing Refinement set up failure. Failed to find restrained for: 
LIG. Please suggest.


Thanks and Regards,

Dipankar




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--
J. Preben Morth, Ph.D
Group Leader
Membrane Transport Group
Nordic EMBL Partnership
Centre for Molecular Medicine Norway (NCMM)
University of Oslo
P.O.Box 1137 Blindern
0318 Oslo, Norway

Email: j.p.mo...@ncmm.uio.no
Tel: +47 2284 0794

http://www.jpmorth.dk

Re: [ccp4bb] very informative - Trends in Data Fabrication

[jens Preben Morth]

For the latest documentary on trolls in Norway see
http://www.imdb.com/title/tt1740707/

The documentary describes both the classification system of Norwegian 
Trolls and why they are sensitive to sun light,  i.e turn to stone.
Depending in the species, some Trolls apparently prefer bridges and 
others caves. They all are attracted to christian blood though.

cheers
Preben

On 4/1/12 10:42 PM, Ethan Merritt wrote:

On Sunday, 01 April 2012, Kendall Nettles wrote:

What is the single Latin word for troll?

Kendall


According to Google Translate, it is Troglodytarum.
But I'm dubious.
I thought trolls lived under bridges rather than in caves.
Except for the ones who inhabit the internet, of course.

Ethan


--
J. Preben Morth, Ph.D
Group Leader
Membrane Transport Group
Nordic EMBL Partnership
Centre for Molecular Medicine Norway (NCMM)
University of Oslo
P.O.Box 1137 Blindern
0318 Oslo, Norway

Email: j.p.mo...@ncmm.uio.no
Tel: +47 2284 0794

http://www.jpmorth.dk

[ccp4bb] PhD position Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo

[jens Preben Morth]

*Dear CCP4
*

*Please forward this advertisement to suitable candidates*

*best Preben
*

*
Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, 
University of Oslo*


**

*1 PhD research fellowship*

*Background:*

The Centre for Molecular Medicine Norway (NCMM, www.ncmm.uio.no) was 
established in 2008 as a national partnership institution with the 
European Molecular Biology Laboratory (www.embl.org). NCMM investigates 
and focuses on disease mechanisms in cancer, immune and hematological 
disorders as well as cardiovascular diseases.


A PhD position is available in the laboratory of Dr. Preben Morth. 
Theposition is funded by an NCMM grant and is available immediately. The 
Focus of the research will include membrane protein involved with 
osmoregulation and anion transport in bacteria and higher eukaryotes. 
Projects focus on bicarbonate transport through the plasma membrane and 
the intra cellular complexes involved with their tight control.


**

*The candidate:*

We search for highly motivated individuals holding an MSc, M.D. or 
equivalent degree with an interest in doing a PhD in experimental 
science working in an interactive international environment with 
techniques as outlined above. Applicants with X-ray structural biology 
background will be prioritized. Knowledge on membrane protein 
characterization using biophysical methods will be an advantage.


The University of Oslo has an agreement for all employees, aiming to 
secure rights to research results and intellectual property.


*The application:*

**The application should include:

1)A one-page statement of motivation and research interests

2)CV

3)Copies of Graduation Certificates

4)Names and contact details of 2-3 references (name, relation to 
candidate, e-mail and telephone number)


The position is for three years with a preferred start in May or June 2012.

*For further information:*

http://www.ncmm.uio.no/research/groups/membrane-transport/

http://www.ncmm.uio.no/research/groups/membrane-transport/morth-bio/

*Deadline for applications: *

*April9, 2012 *labeled with *Ref.no.**2012/3375-- PhD research fellow*

 Please follow link for application:

 http://uio.easycruit.com/vacancy/716105/70932?iso=no

Inquiries regarding the positions can be directed to Dr. Preben Morth 
(j.p.mo...@ncmm.uio.no mailto:j.p.mo...@ncmm.uio.no).


Inquiries regarding the application can be directed to Nina Modahl 
(nina.mod...@ncmm.uio.no mailto:nina.mod...@ncmm.uio.no)


--
J. Preben Morth, Ph.D
Group Leader
Membrane Transport Group
Nordic EMBL Partnership
Centre for Molecular Medicine Norway (NCMM)
University of Oslo
P.O.Box 1137 Blindern
0318 Oslo, Norway

Email:j.p.mo...@ncmm.uio.no
Tel: +47 2284 0794

http://www.jpmorth.dk

[ccp4bb] PhD position Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo

[jens Preben Morth]

*Dear CCP4
*

*Please forward this advertisement to suitable candidates*

*best Preben
*

*
Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, 
University of Oslo*


**

*1 PhD research fellowship*

*Background:*

The Centre for Molecular Medicine Norway (NCMM, www.ncmm.uio.no) was 
established in 2008 as a national partnership institution with the 
European Molecular Biology Laboratory (www.embl.org). NCMM investigates 
and focuses on disease mechanisms in cancer, immune and hematological 
disorders as well as cardiovascular diseases.


A PhD position is available in the laboratory of Dr. Preben Morth. 
Theposition is funded by an NCMM grant and is available immediately. The 
Focus of the research will include membrane protein involved with 
osmoregulation and anion transport in bacteria and higher eukaryotes. 
Projects focus on bicarbonate transport through the plasma membrane and 
the intra cellular complexes involved with their tight control.


**

*The candidate:*

We search for highly motivated individuals holding an MSc, M.D. or 
equivalent degree with an interest in doing a PhD in experimental 
science working in an interactive international environment with 
techniques as outlined above. Applicants with X-ray structural biology 
background will be prioritized. Knowledge on membrane protein 
characterization using biophysical methods will be an advantage.


The University of Oslo has an agreement for all employees, aiming to 
secure rights to research results and intellectual property.


*The application:*

**The application should include:

1)A one-page statement of motivation and research interests

2)CV

3)Copies of Graduation Certificates

4)Names and contact details of 2-3 references (name, relation to 
candidate, e-mail and telephone number)


The position is for three years with a preferred start in May or June 2012.

*For further information:*

http://www.ncmm.uio.no/research/groups/membrane-transport/

http://www.ncmm.uio.no/research/groups/membrane-transport/morth-bio/

*Deadline for applications: *

*April9, 2012 *labeled with *Ref.no.**2012/3375-- PhD research fellow*

Inquiries regarding the positions can be directed to Dr. Preben Morth 
(j.p.mo...@ncmm.uio.no mailto:j.p.mo...@ncmm.uio.no).


Inquiries regarding the application can be directed to Nina Modahl 
(nina.mod...@ncmm.uio.no mailto:nina.mod...@ncmm.uio.no)


--
J. Preben Morth, Ph.D
Group Leader
Membrane Transport Group
Nordic EMBL Partnership
Centre for Molecular Medicine Norway (NCMM)
University of Oslo
P.O.Box 1137 Blindern
0318 Oslo, Norway

Email: j.p.mo...@ncmm.uio.no
Tel: +47 2284 0794

http://www.jpmorth.dk

Re: [ccp4bb] Opinion on automation

[jens Preben Morth]

After putting up your quote in the lab, a student quickly replied To do 
and fail is to remember and to understand :-)


On 2/17/12 1:43 PM, Harry Powell wrote:

Hi

In addition to what Poul and Graeme have said, it may be worthwhile attending one 
of the fine protein crystallography schools that are run, where you will hear 
lectures on integration  scaling etc that attempt to explain the basics of 
what's being done, and probably have a couple of practical sessions where you get 
to use the programs under the watchful eye of an expert. Or you could ask someone 
who has taught on (or attended) one of these schools if you could see their lecture 
slides and notes...

to read is to forget, to write is to remember,  to do is to understand .

On 17 Feb 2012, at 11:31, Theresa H. Hsu wrote:


Dear crystallographers

I would like to get some opinion. For someone beginning to learn basic 
crystallography including indexing, scaling ..., should I start with automated 
tool like Xia2? Or is manual method for each step better for learning?

Thank you.

Theresa

Harry
--
Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills Road, 
Cambridge, CB2 0QH


--
J. Preben Morth, Ph.D
Group Leader
Membrane Transport Group
Nordic EMBL Partnership
Centre for Molecular Medicine Norway (NCMM)
University of Oslo
P.O.Box 1137 Blindern
0318 Oslo, Norway

Email: j.p.mo...@ncmm.uio.no
Tel: +47 2284 0794

http://www.jpmorth.dk

Re: [ccp4bb] Choice of wavelength

[jens Preben Morth]

If you are not looking for a specific metal, you can play it safe and 
collect a redundant native data set at 0.9 A and one at 1.5 A, to check 
for Ca,Cl,SO4 etc and other anomalous scatterers

cheers
Preben
On 2/13/12 10:02 PM, Theresa H. Hsu wrote:

Hi all.

When collecting data, is there a specific wavelength to be chosen at 
synchrotron source? Does it make difference between 0.9 and 1.5 A, for example? 
I know it is important for SAD/MAD but how about MIR?

Thank you.

Theresa

[ccp4bb] Early Stage Researcher (PhD Fellowship)

[jens Preben Morth]

Dear ccp4bb
on behalf of Ludvig Sollid, I would like to announce the following PhD 
studentships.
We are seeking to fill two fully funded PhD fellowships (Early Stage 
Researcher, SKO 1017, stipendiat) in the biochemistry and immunology of 
coeliac disease for the Marie Curie Initial Training Networks (ITN) 
Project TRANSPATH. The objective of TRANSPATH is to establish the 
molecular nature of the role of transglutaminases in a variety of human 
diseases including coeliac disease. TRANSPATH is funded by the European 
Framework Programme 7 Marie Curie Actions with the purpose of offering 
early-stage researchers the opportunity to improve their research 
skills, join established research teams and enhance their career prospects.


see more information
http://ec.europa.eu/euraxess/index.cfm/jobs/jobDetails/33752069
People with a structural biology background will have an advantage.

cheers
Preben

Re: [ccp4bb] No Cl- or S Anomalous Signal

[jens Preben Morth]

Hi Jacob
I agree with Juergen, and just add that your Cys and Cl might not be 
fully occupied.

cheers
Preben

On 9/1/11 10:03 PM, Jacob Keller wrote:

Dear Crystallographers,

I recently have been working with a 2.5 Ang SeMet peak wavelength
dataset which contains 2 cys's and also a couple of bona fide Cl ions
(reasonable b-factor/site is semi-buried/water does not work). In the
FFT anomalous difference map using PhiC from the refined model and
Dano, I can see the MSE's at ~10 sigma, but no Cl ions, even though Cl
should have f = ~0.3 versus Se's f = ~4, and no S's in the cys,
despite f = 0.23e. There is really no anomalous peak at all--is it
just the smallness of the signal, or are the Se's somehow swamping
out the other signal? Perhaps the phases are tainted by the presence
of semet in the model?

Looking for suggestions,

Jacob Keller

***
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
cel: 773.608.9185
email: j-kell...@northwestern.edu
***


--
J. Preben Morth, Ph.D
Group Leader
Membrane Transport Group
Nordic EMBL Partnership
Centre for Molecular Medicine Norway (NCMM)
University of Oslo
P.O.Box 1137 Blindern
0318 Oslo, Norway

Email: j.p.mo...@ncmm.uio.no
Tel: +47 2284 0794

http://www.jpmorth.dk

Re: [ccp4bb] Unexplained density near cobalt

[Jens Preben Morth]

hey Mischa
I would guess that is a split cobalt/metal site occupancy 0.1 and 0.9 or 
something like that.  
If you calculate an anomalous difference map you may be able to confirm/reject 
that suggestion, depending on the strength of the anomalous signal.

cheers
Preben  
 
On 07.07.2011, at 17:07, Machius, Mischa Christian wrote:

 Y'all,
 
 I was wondering if anyone had any thoughts about a feature we observe with a 
 metal-binding site: we have a cobalt that is bound by four histidines and one 
 carboxyl group. There is extra density near the cobalt. See pictures below. 
 The extra density spans the NE2 atoms from two histidines. The Fo-Fc peak 
 (green) has a height of up to 10 sigma (eight molecules in the asymmetric 
 unit, all showing the same feature).
 
 I placed a water molecule into the density to get some distances: the 
 distances between the peak and the neighboring histidine NE2 atoms is ~1.8Å 
 and ~2.0Å, resp. The distance between the peak and the cobalt is ~1.7Å. The 
 resolution is 1.24Å.
 
 Any input would be greatly appreciated.
 
 Many thanks in advance!
 
 Cheers!
 MM
 
 
 Screen shot 2011-07-07 at 9.44.43 AM.pngATT1.cScreen shot 2011-07-07 
 at 9.44.55 AM.png

J. Preben Morth, Ph.D
Group Leader
Membrane Transport Group
Nordic EMBL Partnership
Centre for Molecular Medicine Norway (NCMM)
University of Oslo
P.O.Box 1137 Blindern
0318 Oslo, Norway

Email: j.p.mo...@ncmm.uio.no
Tel: +47 2284 0794

http://www.jpmorth.dk

Re: [ccp4bb] How to get anomalous signal for Ca

[Jens Preben Morth]

Dear Xianchidong
If you are sure it is a divalent ion, Mg would be hard to detect even at
a wavelength of 2.07A.
best
Preben

xianchidong wrote:
 Dear All:
 When I solved the crystal structure of protein, I found a metal
 binding in it. But however, I can not decide which type of atom it is.
 I tried ICP-AES and the result suggested the protein contained Ca. I
 tried to get anomalous signal at the wavelength of 2.07A. And I
 collected the 360 degree with the spacegroup P6 and the average
 redundancy is 19.6. But still I can not see the anomalous signal for
 that metal even I can see clearly the anomalous signal for sulfur.
 Does anybody have suggestions for me?
 Thanks in advance.
 2009-06-30
 
 xianchidong


-- 
Jens Preben Morth, Ph.D
Aarhus University
Department of Molecular Biology
Gustav Wieds Vej 10 C
DK - 8000 Aarhus C
Tel. +45 8942 5257, Fax. +45 8612 3178
j...@mb.au.dk
website: http://person.au.dk/da/j...@mb

Re: [ccp4bb] dry shipper on airplaine

[Jens Preben Morth]

Hi Clemens
We normally check in the dewar as normal luggage after we have removed all
liquids, we have never had any problems travelling from Aarhus to SLS.
just remind the students coming along not to mention movies like Twelve
monkeys or outbreak when checking it in.
best Preben

 Dear all,

 I wonder if it would be still/again possible to check in a dry shipper for
 a
 flight inside Europe. What is your experience?

 Cheers,
 Clemens