[ccp4bb] Antiviral research: PhD students wanted

2022-09-20 Thread Grant Hansman 
We are looking for PhD students funded or willing to apply for internal 
funding. Situated near the beautiful Gold Coast beaches in sunny Queensland, 
Australia. Our lab is located at the Institute for Glycomics at Griffith 
University. We have several PhD projects available.

We will use a multidisciplinary approach to develop Nanobodies against 
norovirus and lagovirus, including bioinformatics, X-ray crystallography, 
molecular biology techniques, cell culture.

Projects:
(a) Precisely identify essential co-factor binding sites and epitope map 
norovirus capsids using Nanobodies targeting clinically relevant and emerging 
noroviruses.
(b) Produce broadly reactive norovirus Nanobodies and develop novel 
Nanobody-based RATs.
(c) Generate norovirus Nanobody-based therapeutics targeting co-factor sites 
and other vulnerable regions on the capsid.

1.  Koromyslova AD, Devant JM, Kilic T, Sabin CD, Malak V, Hansman GS. 
2020. Nanobody-Mediated Neutralization Reveals an Achilles Heel for Norovirus. 
J Virol 94.10.1128/jvi.00660-20
2.  Ruoff K, Kilic T, Devant J, Koromyslova A, Ringel A, Hempelmann A, 
Geiss C, Graf J, Haas M, Roggenbach I, Hansman G. 2019. Structural Basis of 
Nanobodies Targeting the Prototype Norovirus. J Virol 
doi:10.1128/JVI.02005-18.10.1128/JVI.02005-18
3.  Koromyslova AD, Hansman GS. 2017. Nanobodies targeting norovirus capsid 
reveal functional epitopes and potential mechanisms of neutralization. PLoS 
Pathog 13:e1006636.10.1371/journal.ppat.1006636
4.  Koromyslova AD, Hansman GS. 2015. Nanobody binding to a conserved 
epitope promotes norovirus particle disassembly. J Virol 
89:2718-2730.10.1128/JVI.03176-14

Requirements:
•   Experience in protein structural biology

•   Experience in protein expression and purification

•   Excellent knowledge in protein structural biology

•   Participation in all stages of the structure determination

•   Demonstrated independent thought/creativity in science. 


Interested applicants should send CV and statement of interest to Grant 
Hansman: g.hans...@griffith.edu.au

https://experts.griffith.edu.au/26877



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[ccp4bb] Positions Open for Academic Staff Scientists in Stanford’s SyneRx Center’s Structural Biology Core

2022-09-20 Thread Dunn, Lisa B. 
Academic Staff Scientist in Stanford’s SyneRx Center’s Structural Biology Core

Job Description:
The SyneRx Center at Stanford University is one of nine National Antiviral Drug 
Discovery Centers for Pathogens of Pandemic Concern (AViDD) recently funded by 
the National Institute for Allergy and Infectious Diseases. We are seeking to 
appoint two Ph.D. level scientists that will bring complementary research 
experience in cryoEM/ET and synchrotron-enabled x-ray techniques, primarily 
macromolecular crystallography. Stanford’s SyneRx Center includes a Structural 
Biology Core (SBC) to provide state-of-the-art tools and capabilities for 
structural determinations from RNA and proteins to virus and virus infected 
cells. This SBC is comprised of three Subcores including protein production (at 
Stanford University campus facilities and labs), x-ray crystallography and 
scattering (at the Stanford Synchrotron Radiation Lightsource), and cryogenic 
electron microscopy and tomography (cryoEM/ET at facilities located at SLAC 
National Accelerator Laboratory).
As a staff scientist, you would work collaboratively to drive all aspects of 
the three Subcores in the SBC, specifically through interacting with scientists 
in the research teams and providing coordination in areas that include sample 
preparation and characterization, data acquisition, modeling and structure 
determination and validation, pipe-line organization and feedback.  You would 
also assist and train the SyneRx Center’s Project scientists in performing the 
structure characterizations to facilitate and accelerate the design of novel 
and effective antivirals against SARS-CoV-2 and other RNA viruses of pandemic 
potential.  Driving new developments in innovative approaches to obtaining and 
applying high throughput structure-based cryoEM/ET and x-ray methods would also 
be a goal of your research. You would be interacting with other staff 
scientists in the vibrant research organization that comprises the structural 
biology programs for x-rays (SSRL) and cryoEM at SLAC and Stanford, and also 
have a strong role within the SyneRx Center to provide knowledge and services 
as well as bridge and coordinate between the many entities.  You would be 
cross-trained in the structural methods.  The work will require being 
accessible occasionally outside of regular working hours.

Qualifications:

A Ph.D. degree in biophysics, structural biology, biochemistry or a related 
field and post-doctoral experience in the use of x-ray macromolecular 
crystallography, and/or cryoEM/ET.  Other required qualifications include:

· Experience in biochemical purification and sample preparation.

· Experience in data collection, processing and analysis of 
macromolecular crystallography and/or cryoEM data up to structural solutions 
and validation of results.

· Excellent communications and organizational skills.

· The ability to work both independently and collaboratively in a team.
Desired Qualifications/Skills:

· Experience with biological small angle x-ray scattering/diffraction 
is desirable as applicable.

· A track record of scientific productivity through publications in 
relevant fields.

· Experience with computer tools in data management and image analysis.

· Strong communication skills demonstrated through teaching roles 
and/or invited lectures at conferences.
Stanford is an equal employment opportunity and affirmative action employer.  
All qualified applicants will receive consideration for employment without 
regard to race, color, religion, sex, sexual orientation, gender identity, 
national origin, disability, protected veteran status, or any other 
characteristic protected by law. Stanford welcomes applications from all who 
would bring additional dimensions to the University's research mission.

For additional information on our research activities, please visit
https://www.nih.gov/news-events/news-releases/nih-announces-antiviral-drug-development-awards
https://med.stanford.edu/news/all-news/2022/06/jeffrey-glenn-grant.html 
https://cryoem.slac.stanford.edu/
http://smb.slac.stanford.edu/
Please send your application, CV and the names of three references with contact 
information to Ms. Evelyn Castaneda, 
evel...@slac.stanford.edu.




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[ccp4bb] Session on mix-and-inject serial crystallography at the SSRL/LCLS Users' Meeting

2022-09-20 Thread Mark Wilson 
Dear fellow structural biologists,
Dr. Chris Kupitz (LCLS) and I are co-hosting a session on mix-and-inject serial 
crystallography at XFELS and synchrotrons on Weds, 9/28 as part of this year’s 
SSRL/LCLS Users’ Meeting.  This is an opportunity to hear from leading 
researchers about new methods and results featuring this exciting technique.  
The agenda is here: 
https://events.bizzabo.com/SLAC-UsersMeeting-2022/agenda/session/910608
The meeting is fully remote this year and registration is still open 
(https://events.bizzabo.com/SLAC-UsersMeeting-2022/home).

Best regards,
Mark

Mark A. Wilson (he/him)
Professor
Department of Biochemistry/Redox Biology Center
University of Nebraska
N118 Beadle Center
1901 Vine St.
Lincoln, NE 68588




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Re: [ccp4bb] Help with isomer ligand from PDB database

2022-09-20 Thread Paul Emsley 

On 17/09/2022 15:48, Marion Schuller wrote:
>
>  
>
> Dear CCP4bb community,
>
>  
>
> I am writing regarding a problem with the refinement of an isomer
> ligand. I try to refine a structure which has the ligand “Carba-NAD”
> (as beta isomer) bound. This ligand is already in the pdb database as
> “CNA”. Although the ligand is in its beta-Carba-NAD form in the
> database, it is loaded into WinCoot as alpha isomer. When generating
> the restraints of Carba-NAD (via the grade server, calling it also
> “CNA”), I can load and refine the correct beta isomer ligand as long
> as I provide the grade-generated .cif file otherwise it would refine
> it back to the alpha isomer. Yet, in the preliminary preparation of
> the wwPDB X-ray validation report for structure deposition, the
> message flags up that the ligand “could not be matched to an existing
> wwPDB Chemical Component Dictionary definition”. With an older ccp4
> version in the background, I noticed that WinCoot would however load
> the beta isomer and I am now wondering if this problem lies in the
> .cif file of the new ccp4 library. Is there a possibility to
> check/correct the CNA file in the current ccp4 library or would there
> be a different way for solving this problem? I would be very grateful
> for support and help!
>
>  
>
Dear Marion,

As a rule, if a molecule has a different anomericity it has a different
ligand-id (three-letter-code) in the CCD. It seems to me that you need a
new entry in the CCD. It is a good thing that the wwPDB X-ray validation
flags this up as a ligand that matched with and existing entry.

So take the entry for CNA:

https://files.rcsb.org/ligands/view/CNA.cif

change the stereo_config from S to an R for C2D (I am guessing that that
is the anomeric carbon atom) in the atom table. Then feed that to
Acedrg. (I'd chop off the _pdbx_chem_comp_descriptor block so that that
Acedrg doesn't get distracted by the out of date SMILES).

Using that dictionary your refinement should be smooth sailing.

Upon deposition, the wwPDB will then reward you with one of the last
ever three letter codes - hooray!


Paul





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[ccp4bb] JOB IN SCIENTIFIC ILLUSTRATION AT THE MRC LABORATORY OF MOLECULAR BIOLOGY (LMB), CAMBRIDGE

2022-09-20 Thread David Barford 
JOB OPPORTUNITY FOR A SCIENTIFIC ILLUSTRATOR AND ANIMATOR AT THE MRC LABORATORY OF MOLECULAR BIOLOGY (LMB), CAMBRIDGE, UKWe are looking for a Scientific Illustrator and Animator to join the VisLab team at the LMB. The role holder will create innovative and intriguing 2D and 3D still and animated graphics for visualisation and communication of the LMB’s exceptional science and research, preferably using Blender. If you have experience or know anybody who has, and are interested to pursue this field and join the team, please contact Shraddha Nayak sna...@mrc-lmb.cam.ac.uk for more details. The goal of the VisLab team is to help visualise and communicate LMB's compelling science On behalf of Shraddha Nayak (sna...@mrc-lmb.cam.ac.uk)Please see attached for more details.

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LMBVisLab_SciIllustratorAnimator.pdf
Description: Adobe PDF document
__Dr. David BarfordStructural Studies DivisionMRC Laboratory of Molecular BiologyFrancis Crick AvenueCambridge CB2 0QH, UK.e.mail: dbarf...@mrc-lmb.cam.ac.ukTel. +44 (0)1223 26707507919 927824 (M)



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[ccp4bb] AW: Multiplicity is more than 20

2022-09-20 Thread Schreuder, Herman /DE 
Hi Prasun,

As others have pointed out, the higher the multiplicity, the better, so I would 
be happy about it and not worry.
Concerning the higher Rwork in the inner shell, what are the resolution limits 
of this shell? Are there any ice-rings within these resolution limits? 
Otherwise I would check if there are no overloaded reflections in your data 
set, since a few rogue strong reflections may wreak havoc on your Rfactors.

Best, Herman

Von: CCP4 bulletin board  Im Auftrag von Prasun Kumar
Gesendet: Montag, 19. September 2022 20:30
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [ccp4bb] Multiplicity is more than 20

Hi All:

I have collected a dataset for a crystal of a 30 residues long helical peptide 
that makes a trimer in the solution. I also solved the structure to get a 
trimer. My issues start when I start preparing for a deposition.

Details about the data:

space group: I 21 3
Resolution: 1.6
Current Rfree/ Rwork: 0.21/0.19

Problems:
According to Aimless, Multiplicity: 33.9, and I understand that the value 
should be less than or equal to 20. Does it mean that I have a lot of random 
noise or ice rings or something similar?
For the inner shell, R work is also higher than R free.

Please guide me in solving the above issue.

Thank You
Prasun




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Re: [ccp4bb] Multiplicity is more than 20

2022-09-20 Thread Dale Tronrud 

   Okay, I weigh in on the R factor issue...

   The free R that we calculate is only an estimate of the "true free 
R".  What we really want to know is what would the R value be if there 
there was no "bias" to the atomic model.  We make this estimate by 
pulling a subset of the data out of the refinement.  If you pull out a 
different subset you will get a somewhat different "free R estimate".


   If you run a lot of refinement with different subsets you will get a 
distribution of "free R estimates" and that distribution will have a 
standard deviation.  The smaller the number of reflections in the subset 
the larger that standard deviation will be.


   One shell of data will have only a few reflections so the standard 
deviation will be large and a particular instance may very well have a 
value for the "free R estimate" that is smaller than the working R, 
particularly when the overall R values are similar as in your refinement.


Dale Tronrud

On 9/19/2022 11:30 AM, Prasun Kumar wrote:

Hi All:

I have collected a dataset for a crystal of a 30 residues long helical 
peptide that makes a trimer in the solution. I also solved the structure 
to get a trimer. My issues start when I start preparing for a deposition.


Details about the data:

space group: I 21 3
Resolution: 1.6
Current Rfree/ Rwork: 0.21/0.19

Problems:
According to Aimless, Multiplicity: *33.9*, and I understand that the 
value should be less than or equal to 20. Does it mean that I have a lot 
of random noise or ice rings or something similar?

For the inner shell, R work is also *higher* than R free.

Please guide me in solving the above issue.

Thank You
Prasun




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