Re: [ccp4bb] Some sort of "closure"?

[Keller, Jacob]

Wow, something really happened! I wonder how many citations of those 
articles/structures are out there? 1000? I hadn't realized it was more than 
just that Nature paper. I hope nothing important is built on them.

JPK

+
Jacob Pearson Keller
Research Scientist / Looger Lab
HHMI Janelia Research Campus
19700 Helix Dr, Ashburn, VA 20147
Desk: (571)209-4000 x3159
Cell: (301)592-7004
+

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From: CCP4 bulletin board  On Behalf Of Mark J van Raaij
Sent: Thursday, July 19, 2018 7:59 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Some sort of "closure"?

Not sure if this has been posted here yet, but I don't remember it and only 
just saw this:
https://www.federalregister.gov/documents/2018/04/16/2018-07782/findings-of-research-misconduct
[it's about the famous case of fabricated structures and structure factors]

Mark J van Raaij
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia - CSIC
calle Darwin 3
E-28049 Madrid, Spain
tel. (+34) 91 585 4616
http://wwwuser.cnb.csic.es/~mjvanraaij
Editor of Acta Crystallographica F, Structural Biology Communications
http://journals.iucr.org/f/




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Re: [ccp4bb] unidentified electron density

[Bernhard Rupp]

Another plug (with a PEG list, Table 4 Figure 5):
http://journals.iucr.org/d/issues/2016/12/00/rr5136/index.html

Best, BR


-Original Message-
From: CCP4 bulletin board  On Behalf Of Robbie Joosten
Sent: Thursday, July 19, 2018 3:10 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] unidentified electron density

Hi Harsh,

Just try a slightly longer PEG molecule: PGE (in PDB nomenclature). That's the 
version with 3 glycol units. Others are (in order of increasing size) PG4, 1PE, 
P6G, P33, PE8, 2PE, XPE, 12P, 33O, and P3E. This list comes from a paper that 
shows that PEG can go to all sorts of nasty sites: 
https://onlinelibrary.wiley.com/doi/full/10.1002/pro.2923 (yes, that is a bit 
of a plug).

Cheers,
Robbie

> -Original Message-
> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of 
> Harsh Bansia
> Sent: Thursday, July 19, 2018 09:06
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [ccp4bb] unidentified electron density
> 
> Dear All
> 
> I am refining a 1.63 Angstrom data set for a methyltransferase for 
> which methyl-accepting substrate is not known. I came across a density 
> in the putative substrate binding site in which i have modeled a PEG 
> molecule as shown in  attached screen shots.  The crystallization 
> condition includes MgCl2, Tris-HCL and PEG3350.
> The current Rwork/Rfree is 15.2/18.6. The average B-factor of fitted 
> PEG molecule is 40 while that of surrounding residues is 20.
> 
> 
> Any suggestions regarding interpretation of this density would be much 
> appreciated.
> 
> 
> Thank you
> 
> Regards
> Harsh
> 
> 
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1




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[ccp4bb] Job Opportunity at Rheos Medicines

[Brian Albrecht]

Dear ccp4 community,

Rheos Medicines, a newly formed start-up from Third Rock Ventures, is seeking a 
structural biologist with industrial experience to join our team.  Please reply 
to the posting below – only inquiries to the posting will be responded to.

https://rheosrx.com/our-workplace/careers/associate-director-structural-biology/

Sincerely,
Brian


Title: Associate Director, Structural Biology
Department: Drug Discovery
Reports To: VP, Drug Discovery
Location: Cambridge, MA

The Company:

At Rheos, we are leading the way in the emerging field of immunometabolism to 
discover novel medicines to treat inflammatory-mediated  diseases, including 
autoimmune diseases. Our medicines control metabolic pathways of immune cells 
that influence their activation state, in order to rebalance immune responses 
that cause inflammation or autoimmunity.

The Role:

The Associate Director, Structural Biology, will provide leadership and 
expertise in the structural characterization of Rheos’s drug targets. The ideal 
candidate will be focused on protein crystallography but will integrate with 
the drug discovery organization to implement a variety of biophysical 
techniques.

Major Responsibilities:

  *   Collaborate with colleagues in lead discovery, biology, and chemistry to 
develop a structural biology strategy.
  *   Designing biophysics-grade protein constructs and assisting in the 
optimization of purification protocols.
  *   Crystallization, X-ray structure determination, and analysis of important 
drug targets through working with external collaborators.
  *   Management of external structural biology collaborations (CROs)
  *   Providing regular updates to cross-functional teams and helping guide 
structure-based compound design in close collaboration with chemistry group.

Requirements and Qualifications:

Education:

  *   PhD degree structural biology or biophysics

Required Experience:

  *   7+ years of drug discovery experience in a pharmaceutical/biotechnology 
setting;
  *   Demonstrated ability to solve difficult problems in protein 
crystallography, structural biology and biophysics
  *   Demonstrated competency in protein construct design and expression and 
purification strategies using bacterial, insect, and mammalian hosts.

Knowledge, Skills & Abilities:

  *   Strong knowledge of the drug discovery process, with deep experience in 
implementing hit identification strategies through candidate selection;
  *   Extensive knowledge of protein structure and function, with the ability 
to articulately communicate structural information to a broad audience.
  *   Experience with other structural techniques (e.g. electron microscopy, 
small-angle X-ray scattering) is preferred.

If this excites you, please submit your CV with the title of the position in 
the subject line to care...@rheosrx.com



This email and any attachments may contain CONFIDENTIAL or PRIVILEGED 
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Rheos Medicines, Inc. If you have received this email in error, distributing, 
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Rheos Medicines, Inc. If you have received this email in error, distributing, 
copying, using or disclosing its contents is prohibited. Please notify us of 
the delivery error by replying to this message and then delete it from your 
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This email and any attachments may contain CONFIDENTIAL or PRIVILEGED 
information and is a private communication between the intended addressee
and Rheos 

[ccp4bb] Some sort of "closure"?

[Mark J van Raaij]

Not sure if this has been posted here yet, but I don't remember it and only 
just saw this:
https://www.federalregister.gov/documents/2018/04/16/2018-07782/findings-of-research-misconduct
 

[it's about the famous case of fabricated structures and structure factors]

Mark J van Raaij
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia - CSIC
calle Darwin 3
E-28049 Madrid, Spain
tel. (+34) 91 585 4616
http://wwwuser.cnb.csic.es/~mjvanraaij
Editor of Acta Crystallographica F, Structural Biology Communications
http://journals.iucr.org/f/





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

[ccp4bb] PhD and Postdoc Positions in Structural Biology

[Clemens Grimm]

A PhD and a postdoc position in structural biology is available at the  
department of biochemistry at the Biocentre (head Prof. Utz Fischer)  
of the Julius Maximilians University, Wuerzburg/Germany in the field  
of RNP biochemistry.


The successful applicant will establish protocols for the isolation  
and reconstitution of preparative amounts of RNP complexes, which will  
then be characterized by cryo-electron microscopy and x-ray  
crystallography. We are looking for candidates with expertise in  
protein expression and purification and a strong interest in  
structural biochemistry. Prior knowledge of cryo electron microscopy,  
protein crystallography or biophysical methods is a plus.

Please send your application including a letter of interest,
curriculum vitae, academic certificates and the name and contact  
detail of at least one referee to


Prof. Utz Fischer/Dr. Clemens Grimm
e-mail: clemens.gr...@biozentrum.uni-wuerzburg.de
Lehrstuhl für Biochemie
Biozentrum der Universitaet Wuerzburg
Am Hubland
D-97074 Wuerzburg



--
Dr. Clemens Grimm
Institut für Biochemie
Biozentrum der Universität Würzburg
Am Hubland
D-97074 Würzburg
Germany
e-mail: clemens.gr...@biozentrum.uni-wuerzburg.de
phone : +49 0931 31 84031
-



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Re: [ccp4bb] unidentified electron density

[Robbie Joosten]

Hi Harsh,

Just try a slightly longer PEG molecule: PGE (in PDB nomenclature). That's the 
version with 3 glycol units. Others are (in order of increasing size) PG4, 1PE, 
P6G, P33, PE8, 2PE, XPE, 12P, 33O, and P3E. This list comes from a paper that 
shows that PEG can go to all sorts of nasty sites: 
https://onlinelibrary.wiley.com/doi/full/10.1002/pro.2923 (yes, that is a bit 
of a plug).

Cheers,
Robbie

> -Original Message-
> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
> Harsh Bansia
> Sent: Thursday, July 19, 2018 09:06
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [ccp4bb] unidentified electron density
> 
> Dear All
> 
> I am refining a 1.63 Angstrom data set for a methyltransferase for which
> methyl-accepting substrate is not known. I came across a density in the
> putative substrate binding site in which i have modeled a PEG molecule as
> shown in  attached screen shots.  The crystallization condition includes
> MgCl2, Tris-HCL and PEG3350.
> The current Rwork/Rfree is 15.2/18.6. The average B-factor of fitted PEG
> molecule is 40 while that of surrounding residues is 20.
> 
> 
> Any suggestions regarding interpretation of this density would be much
> appreciated.
> 
> 
> Thank you
> 
> Regards
> Harsh
> 
> 
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1




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https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1

[ccp4bb] Research Associate vacancy at Confo Therapeutics

[Alessandra Beltrami]

Dear All,

There is an opportunity to join the Structural Biology team at Confo 
Therapeutics based in Ghent (Belgium) as Research Associate.
Please see the advert in the link below. Interested candidates should apply 
forwarding a short motivation letter and CV to 
care...@confotherapeutics.com.

http://files8.design-editor.com/93/9333026/UploadedFiles/7CF5EF39-B19A-4DFA-6C1C-D30A3642FD8B.pdf

I thank you in advance.

Best wishes,
Alessandra


Alessandra Beltrami, PhD

Scientist Structural Biology



Confo Therapeutics

Technologiepark 4, 9052 Zwijnaarde

t:+32 (0)9 261 06 71

m:+32 (0)471 47 32 06

alessandra.beltr...@confotherapeutics.com

www.confotherapeutics.com

[cid:image003.png@01D0BB18.EB964F10]

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[ccp4bb] Postdoc position in Heidelberg, Germany

[Grant]

Help develop antivirals against human norovirus using techniques such as X-ray 
crystallography, cryo-EM, molecular biology, and cell culture. Experience in 
structural biology, especially X-ray crystallography required. Our lab is fully 
equipped to carryout most experiments in the drug development. You will have 
opportunities to travel to international collaborators, including Australia, 
Japan, and the USA. We have a great working environment and plenty of freedom 
to explore your own projects and ideas.



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