Re: [ccp4bb] help identifying unknown density

[Federico Forneris]

Any chances for some guadinium leftover from a refolding protocol? 
See second line in fig 1 here, quite similar stacking: 
http://www.mdpi.com/1420-3049/20/5/9214/htm

Best,
F.

Federico Forneris, PhD

The Armenise-Harvard Laboratory of Structural Biology
Dept. Biology and Biotechnology
University of Pavia
Via Ferrata, 9
I-27100 Pavia - ITALY
http://fornerislab.unipv.it






-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Stephen 
Cusack
Sent: lunedì 9 ottobre 2017 17:40
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] help identifying unknown density

Dear All,

 �� I am refining the crystal structure of an E. coli expressed protein 
at 2.65 A resolution. The crystals grew in

0.1 M MES pH6, 0.7 M sodium formate pH 6. Ni-NTA was used in the 
purification.

There are four molecules in the asymmetric unit. A particular histidine 
in each molecular has clear, strong extra density which looks like a 
metal bonded to an imidazole nitrogen (distance approx 2 A) with three 
other co-ordinating atoms in a triangular planar arrangement (see 
attached screen shot for unbiased extra density, atoms are only put in 
the density for illustrative purposes).

Has anyone seen anything like this ? Any suggestions ?

thanks very much

Stephen

-- 

**
Dr. Stephen Cusack, FRS
Head of Grenoble Outstation of the European Molecular Biology Laboratory (EMBL)
Group leader in structural biology of protein-RNA complexes and viral proteins
**

Email:  cus...@embl.fr  
Website: http://www.embl.fr 
Tel:(33) 4 76 20 7238Secretary (33) 4 76 20 7123

Fax:(33) 4 76 20 7199   
Postal address:   EMBL Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, 
38042 Grenoble Cedex 9, France
Delivery address: EMBL Grenoble Outstation, Polygone Scientifique, 71 Avenue 
des Martyrs, 38000 Grenoble, France
**

[ccp4bb] Job advertisement: Researcher/Postdoc BioMAX (1 year employment)

[Uwe Müller]

For the collaboration at the BioMAX beam line at MAX IV Laboratory, Lund, 
Sweden, we are opening this position:
Lunds universitet, MAX IV, Diffraction & Scattering

Lund University was founded in 1666 and is repeatedly ranked among the world’s 
top 100 universities. The University has 42 000 students and 7 400 staff based 
in Lund, Helsingborg and Malmö. We are united in our efforts to understand, 
explain and improve our world and the human condition.

MAX IV is a national large-scale research laboratory providing scientists from 
Sweden and the rest of the world with instruments for research in areas such as 
materials science, structural biology, chemistry and nanotechnology. Fully 
developed it will receive more than 2 000 scientists annually. 200 people are 
currently employed at the MAX IV Laboratory.

Tasks

The tasks include:

- Shared responsibility for the support of academic and industrial users during 
their experimental beam time
- Shared activities in the commissioning of the beamline and its end-station
- Development of the beamline in close collaboration with the MX team and and 
MAX IV staff
- Carrying out diffraction experiments and data evaluations using serial 
crystallography enviroments
- Participation within the training program of the BioMAX/MicroMAX user 
communities
- Contributions to the in house research activities alongside the goal settings 
and activities of the MX group
- Development of the MX user communities

Qualifications

The successful candidate must have the follwing qualfications:

- PhD in natural sciences
- Practical experiences in carrying out synchrotron based single crystal x-ray 
diffraction experiments of bio-macromolecules
- Proven track in completing structural biology projects
- Solid knowledge and experiences in scientific computing
- Demonstrated ability to work independently
- Excellent oral and written command of English
- Very good communication and team working skills

The following qualifications are considered as an asset:

- Experiences with serial crystallograhy sample environments and their 
applications at synchrotron beamlines or XFEL
- Knowledge of synchrotron instrumentations
- Programming skills for controling scientific instruments and data evaluations
- Experiences in synchrotron related user support

This is a 1 year temporary employment.

Lund University welcomes applicants with diverse backgrounds and experiences. 
We regard gender equality and diversity as a strength and an asset.
We kindly decline all sales and marketing contacts.

For further information, please visit:
https://lu.mynetworkglobal.com/en/what:job/jobID:171227/type:job/where:4/apply:1

Uwe & the BioMAX team

Uwe Mueller
Group manager diffraction & scattering beamlines
BioMAX beam line manager

MAX IV Laboratory
Lund University
P.O. Box 118, SE-221 00 Lund, Sweden
Visiting address: Fotongatan 2, 225 94 Lund
Mobile:  +46(0)730-655268
E-mail: uwe.mul...@maxiv.lu.se
Url: www.maxiv.se

Re: [ccp4bb] help identifying unknown density

[Eleanor Dodson]

Any anomalous signal?
Eleanor

On 9 October 2017 at 17:05, Gang Dong  wrote:

> Could it be a formate ion (HCO2−)? _Gang
>
> -Original Message-
> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
> Stephen Cusack
> Sent: Monday, October 09, 2017 5:40 PM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [ccp4bb] help identifying unknown density
>
> Dear All,
>
> I am refining the crystal structure of an E. coli expressed protein at
> 2.65 A resolution. The crystals grew in
>
> 0.1 M MES pH6, 0.7 M sodium formate pH 6. Ni-NTA was used in the
> purification.
>
> There are four molecules in the asymmetric unit. A particular histidine in
> each molecular has clear, strong extra density which looks like a metal
> bonded to an imidazole nitrogen (distance approx 2 A) with three other
> co-ordinating atoms in a triangular planar arrangement (see attached screen
> shot for unbiased extra density, atoms are only put in the density for
> illustrative purposes).
>
> Has anyone seen anything like this ? Any suggestions ?
>
> thanks very much
>
> Stephen
>
> --
>
> **
> Dr. Stephen Cusack, FRS
> Head of Grenoble Outstation of the European Molecular Biology Laboratory
> (EMBL) Group leader in structural biology of protein-RNA complexes and
> viral proteins
> **
>
> Email:  cus...@embl.fr
> Website: http://www.embl.fr
> Tel:(33) 4 76 20 7238Secretary (33) 4 76 20 7123
> Fax:(33) 4 76 20 7199
> Postal address:   EMBL Grenoble Outstation, 71 Avenue des Martyrs, CS
> 90181, 38042 Grenoble Cedex 9, France
> Delivery address: EMBL Grenoble Outstation, Polygone Scientifique, 71
> Avenue des Martyrs, 38000 Grenoble, France
> **
>

Re: [ccp4bb] help identifying unknown density

[Gang Dong]

Could it be a formate ion (HCO2−)? _Gang

-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Stephen 
Cusack
Sent: Monday, October 09, 2017 5:40 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] help identifying unknown density

Dear All,

I am refining the crystal structure of an E. coli expressed protein at 2.65 
A resolution. The crystals grew in

0.1 M MES pH6, 0.7 M sodium formate pH 6. Ni-NTA was used in the purification.

There are four molecules in the asymmetric unit. A particular histidine in each 
molecular has clear, strong extra density which looks like a metal bonded to an 
imidazole nitrogen (distance approx 2 A) with three other co-ordinating atoms 
in a triangular planar arrangement (see attached screen shot for unbiased extra 
density, atoms are only put in the density for illustrative purposes).

Has anyone seen anything like this ? Any suggestions ?

thanks very much

Stephen

-- 

**
Dr. Stephen Cusack, FRS
Head of Grenoble Outstation of the European Molecular Biology Laboratory (EMBL) 
Group leader in structural biology of protein-RNA complexes and viral proteins
**

Email:  cus...@embl.fr  
Website: http://www.embl.fr 
Tel:(33) 4 76 20 7238Secretary (33) 4 76 20 7123

Fax:(33) 4 76 20 7199   
Postal address:   EMBL Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, 
38042 Grenoble Cedex 9, France
Delivery address: EMBL Grenoble Outstation, Polygone Scientifique, 71 Avenue 
des Martyrs, 38000 Grenoble, France
**

[ccp4bb] iNext access to Enhanced support for SAXS and crystallization/serial,crystallography at EMBL Hamburg

[margret]

Dear all,

I would like to draw attention to the availability of enhanced support 
for sample preparation and characterization for SAXS and macromolecular 
crystallography at EMBL Hamburg. For SAXS, this includes biophysical 
characterization and optimization of samples, access to the P12 BioSAXS 
beamline and, if needed, assistance in data analysis. For MX,
the access includes high-throughput crystallization, automatic crystal 
harvesting and data collection on the EMBL beamlines P13 and P14.


The point of access for support is the Sample Preparation & 
Characterization (SPC) facility:


https://www.embl-hamburg.de/services/spc/index.html

Researchers within the European research area can apply for sponsored 
access through iNEXT, which includes sample shipment, travel from the 
home lab and all consumables:


http://www.inext-eu.org/access/

To obtain iNEXT access, a proposal should be submitted that describes the
biological background and translation research component of the project.
Interested scientists are encouraged first to contact the facility at 
s...@embl-hamburg.de.


Best regards,

Rob Meijers

[ccp4bb] LAST CHANCE: DLS/CCP4 data analysis workshop 2017

[David Waterman]

Hi all,

The application period for this year's DLS/CCP4 workshop has been extended
by one week. So, if you are interested in joining us this December, please
apply by 10 am on Monday the 16th October.

Thanks!

-- David

On 12 September 2017 at 21:44, David Waterman  wrote:

> PhD students, postdocs and early career scientists,
>
> Please consider applying for the fourth joint DLS/CCP4 workshop on MX data
> collection and structure solution, to be held at Diamond Light Source, UK
> from the 30th November to the 7th December 2017.
>
> This course offers the opportunity for you to work alongside leaders in
> the field of MX on data from your own crystals. For more details please
> check here:
>
> http://www.ccp4.ac.uk/schools/DLS-2017/
>
> The application period is now open and will close on the 6th October.
> Applicants will be required to submit a CV/resume, describe their projects
> and obtain a letter of support from a supervisor, so please do not wait
> until the last minute to apply! Those with crystals and/or data will be
> given priority.
>
> Best wishes on behalf of the organisers,
>
> David Waterman (CCP4)
>