Re: [ccp4bb] TWIN?

[Eric Montemayor]

Maybe you have a bimolecular dimer when you expected a unimolecular
hairpin?  It’s happened before :)

https://pubmed.ncbi.nlm.nih.gov/31584014/

Eric



On Tue, Jun 8, 2021 at 10:15 AM Almudena Ponce Salvatierra <
maps.fa...@gmail.com> wrote:

> Hello everyone,
>
> I am working with an RNA-only structure, data are at 3 Angstroms, and at
> first, I thought was in the C2 space group (with 6 molecules in the AU).
>
> I can't finish building! it, because the structure seems to get in the way
> of its neighbor symmetrically! See the attached picture, please! The only 4
> residues that the structure is missing "have to go there", where one
> structure meets the other one. The R factors for this spacegroup are around
> 0.3.
>
> However, Phenix Xtriage suggests the symmetry may be higher. So I reindex
> in P622, do MR with Phaser (trying all possible space groups in that point
> group), and it finds a unique solution in space group P 65 2 2 with TFZ of
> 50 and LLG >3000. Of course, the problem persists (one molecule sort of
> interfering with the neighbor), not only that but also the refinement
> R-factors are substantially higher, 0.37.
>
> I have to say that the refinement maps look better when I am working with
> the C2 spacegroup. I can't understand, though, what is happening at that
> "supposedly interface" between the two molecules. Has anybody experienced
> anything like this in the past? Can it be a twin? Is it something else?
> and... how to fix it?
>
> Thank you very much in advance.
>
> Best wishes,
>
> Almudena
>
> --
>
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[ccp4bb] Facility Staff position at UW-Madison

[Eric Montemayor]

Dear colleagues,

UW-Madison is currently looking for a PhD-level staff scientist to support
its new cryo-EM facility.  More information can be found here:

https://jobs.hr.wisc.edu/cw/en-us/job/501112/assistant-scientist-cryoem-research-center

All inquiries should be directed to Elizabeth Wright (erwrig...@wisc.edu)

--
Eric J. Montemayor
Associate Scientist
Member of USNC/Cr
Department of Biochemistry
University of Wisconsin Madison
433 Babcock Dr. Room 145
Madison, WI 53706



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[ccp4bb] Postdoctoral position at UW-Madison

[Eric Montemayor]

A postdoctoral position is immediately available in the laboratory of
Professor Samuel Butcher at the University of Wisconsin-Madison.

https://biochem.wisc.edu/faculty/butcher

The Butcher laboratory is funded by the NIH to investigate the structure
and function of RNA-protein complexes that regulate gene expression.
Additionally, the lab is currently determining structure activity
relationships for small molecules that regulate non-coding RNAs that play
roles in neurodegenerative diseases.

The Butcher laboratory is part of a vibrant research community at
UW-Madison with state-of-the-art resources, such as the National Magnetic
Resonance Facility at Madison (NMRFAM) and a newly established cryo-EM
facility that will soon house a Titan Krios, Talos Arctica and Aquilos
FIB/SEM electron microscope.

The Butcher laboratory has established expertise in NMR, X-ray
crystallography, SAXS, and myriad biophysical techniques.  Additionally, we
collaborate with local experts in cryo-electron microscopy.  Thus,
postdoctoral trainees in the Butcher lab are in a position to learn any
aspect of contemporary structural biology.

Recent publications:
www.ncbi.nlm.nih.gov/pubmed/30215753
www.ncbi.nlm.nih.gov/pubmed/29717126
www.ncbi.nlm.nih.gov/pubmed/28887445
www.ncbi.nlm.nih.gov/pubmed/27194769
www.ncbi.nlm.nih.gov/pubmed/26655855
www.ncbi.nlm.nih.gov/pubmed/24837192

Requirements are a PhD in biochemistry or related scientific field.  If
interested, please send CV by email to: sebutc...@wisc.edu



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[ccp4bb] Computational cryo-EM faculty position at the Morgridge Institute for Research and UW-Madison

[Eric Montemayor]

Dear Colleagues,

A great faculty-level opportunity between the Morgridge Institute for
Research and the University of Wisconsin-Madison. We seek to hire a
tenure-track assistant/associate/full professor in the broad area of
cryo-EM centered quantitative image processing and analysis. This position
is part of a major campus cryo-EM expansion, comprising new faculty hires
in experimental and computational cryo-EM, and a facility to house four new
cryo-microscopes including Thermo Fisher’s 300 kV Titan Krios, 200 kV Talos
Arctica, 120 kV Talos L120C, and Aquilos cryo-FIB-SEM.

For more information about this post and the application process, please
click the link below. Deadline for applications is December 15, 2018.

Morgridge (computational cryo-EM) -
https://morgridge.org/job-posting/investigator-cryo-em/

For more information about the other cryo-EM related faculty positions,
please click the links below. Each search has its own deadline for receipt
of applications. The positions will remain open until filled.

Biochemistry -
http://jobs.hr.wisc.edu/cw/en-us/job/499479/biochemistry-faculty

Virology -
http://jobs.hr.wisc.edu/cw/en-us/job/499366/virus-proteinnucleic-acid-ultrastructure-imaging-cluster-hire

Bacteriology -
http://jobs.hr.wisc.edu/cw/en-us/job/499304/assistant-professor

For additional information, please contact Liz Wright (erwrig...@wisc.edu).

--
Eric J. Montemayor
Associate Scientist
Department of Biochemistry
University of Wisconsin Madison
433 Babcock Dr. Room 145
Madison, WI 53706



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[ccp4bb] Cryo-EM virology faculty position at UW-Madison

[Eric Montemayor]

Dear Colleagues:



The University of Wisconsin-Madison Institute for Molecular Virology (IMV),
in collaboration with the Department of Biochemistry or the Department of
Plant Pathology, seek to hire a tenure-track (junior) Assistant Professor
to develop a collaborative cutting-edge research program aimed at
understanding the structure, dynamic responses and function of viral
machinery, or virus-host interactions, using biochemical, biophysical, and
structural techniques, especially cryo-electron microscopy (cryo-EM).


This position is one of a three-part synergistic hiring initiative "The
Metastructures of Viral Infection" which will expand and complement the
Madison Virology Program (MVP). This faculty hire will develop a research
program in virology or virus-related cell biology that will take advantage
of the resources available in the new Cryo-EM Research Center. The Center
houses four new cryo-microscopes including Thermo-Fisher's 300 kV Titan
Krios, 200 kV Talos Arctica, 120 kV Talos L120C, an Aquilos cryo-FIB-SEM,
as well as other ancillary preparative equipment.



Please click Here

 for the direct link to the post and application process. The deadline for
receipt of applications is December 1, 2018. The position will remain open
until filled.



For more information, please contact Ann Palmenberg  or  Elizabeth Wright.



--

Eric J. Montemayor

Associate Scientist

Department of Biochemistry

University of Wisconsin Madison

433 Babcock Dr. Room 145

Madison, WI 53706



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Re: [ccp4bb] Off topic -- Job post

[Eric Montemayor]

Hi Xiaoshan,

I am interested in applying, but do you think that an experienced
protein-RNA crystallographer with a physical chemistry background would be
given consideration?  It so, I'll send a CV and cover letter through
official channels.

-- 
Eric J. Montemayor, Ph.D.
Assistant Scientist
University of Wisconsin-Madison
145 Biochemistry Laboratories
433 Babcock Drive
Madison, WI 53706
512.784.5981
https://www.linkedin.com/in/ericmontemayor
<https://www.linkedin.com/pub/eric-montemayor/63/121/98b>
http://about.me/montemayor


On Wed, Mar 25, 2015 at 7:05 PM, Min, Xiaoshan  wrote:

>  Dear friends,
>
>
>
> I would like to draw your attention to an opening in our structural
> biology group at Amgen San Francisco.  Please apply through the web portal
>
>
>
>
> http://careers.amgen.com/en/jobs/descriptions/scientist-protein-biochemist-crystallographer-south-san-francisco-job-5231739
>
>
>
> The job description is at the end of this email.
>
>
>
> Cheers,
>
>
>
> Xiaoshan Min
>
> Molecular Structure
>
> Amgen San Francisco
>
> 650-2442412
>
>
>
>
>
> *Scientist - Protein Biochemist / Crystallographer*
>
> *Auto Req #:* 25895BR
> *Career Categories: *Research
> *Location: *US - CA - South San Francisco
>
> *Amgen Job Description *
>
> Amgen is a leading global biotechnology company, with a mission to serve
> patients around the world. As a science-based, patient-focused
> organization, we discover and develop innovative therapies to treat serious
> illnesses. Our medicines have made a dramatic difference in the lives of
> millions. To underpin our commitment to serve patients, Amgen is expanding
> our Research and Development facilities in South San Francisco, CA (ASF).
>
> We are looking for a highly motivated and talented protein biochemist or
> crystallographer to join the ASF Structural Biology group. This laboratory
> provides comprehensive molecular insight and structure-based design for
> drug target assessment, mechanism of action, protein-protein and
> protein-ligand interactions, as well as protein engineering to facilitate
> drug discovery across various important therapeutic areas. The candidate
> will have the opportunity to contribute directly to the exciting drug
> discovery process through structural studies on a wide variety of important
> biological systems, including human integral membrane proteins.
>
> The candidate will be responsible for leading projects through the entire
> protein crystallographic process, including construct design, protein
> purification, characterization, crystallization, X-ray data collection,
> structure determination and analysis. The candidate will be working closely
> with molecular biologists and protein biochemists in the protein technology
> team. The candidate will also interact directly with computational and
> medicinal chemists and protein engineering teams for structure-based drug
> design projects. The candidate must have strong interpersonal skills to
> work in interdisciplinary project teams
>
> *Basic Qualifications *
>
> - Doctorate degree
> OR
> - Master’s degree & 5 years of scientific experience
> OR
> - Bachelor’s degree & 7 years of scientific experience
>
> *Preferred Qualifications *
>
> - PhD in protein biochemistry, crystallography, or related discipline with
> significant postdoctoral research experience
> - Proven ability to design and perform experiments from protein expression
> to structure determination
> - Knowledge of state-of-the-art membrane protein structural biology
> techniques including all aspects of construct design, expression,
> purification, crystallization screening/optimization (including LCP and
> LCP-FRAP)
> - Expertise in protein biochemical and biophysical characterization
> - Experience with X-ray free electron laser and/or cryo-EM will be highly
> desirable
> - Excellent presentation skills (written and oral) that enhance team-based
> progress are required
> - Ability to work independently and effectively within timelines and to
> collaborate in a multidisciplinary environment
>
> Amgen is an Equal Opportunity/Affirmative Action employer and will
> consider all qualified applicants for employment without regard to race,
> color, religion, sex, national origin, protected veteran status, or
> disability status.
>
>
>

Re: [ccp4bb] ATP library file in REFMAC - Part II

[Eric Montemayor]

L
On Aug 27, 2014 5:12 PM, "Santarsiero, Bernard D."  wrote:

> I appreciate all of the comments and suggestions on how to locate a better
> CIF file for ATP. I adopted the suggestion of Boaz, and generated a new
> ATP.cif file, and refined one of my structures.
>
> The validation server still uses substantially different target bond
> lengths and angles, so there is better agreement, but I still get flags.
> Both bond length and angles target values are more realistic than what was
> used in the REFMAC ATP.cif file, but I still find fault with the target
> values.
>
> For example, the bond lengths and angles around PB, the beta P atom, range
> from 104.4-108.7deg in the "grade" file, and are unrealistic since they
> are all less than the tetrahedral angle. The CIF also targets one P-O as a
> single and the other as formally a double bond, but most crystallographic
> studies indicate at least some delocalization over both internal oxygen
> atoms, and a slight compression of that angle.  The validation server has
> an "ideal" target value of 101.66deg which is surely contracted from a
> more reasonable value near 105deg.
>
> One approach that would be useful is to consider refinement on special
> groups, like phosphate, with structural parameters, instead of actual
> target bond lengths and angles, so R1 for the two PB-O1B and PB-O2B
> distances, and R2 for the two PB-O3A and PB-O3B distances, and pairs of
> angle restraints incorporating a complete delocalization model. See, for
> example, Murray-Rust, Burgi, and Dunitz, J. Am. Chem. Soc., 97, 921
> (1975), or Tamasi at al., The Open Crystallography Journal, 3, 1 (2010).
> This could be used to directly address questions about delocalization and
> hydrolytic capacity, rather than trying to determine then from bond
> lengths.
>
> Bernie
>
>
>
>
> On Wed, August 27, 2014 2:05 pm, Boaz Shaanan wrote:
> >   Or use Grade:
> > http://grade.globalphasing.org/cgi-bin/grade/server.cgi
> >   which gives the correct bond length.
> >   Boaz
> >
> >   Boaz Shaanan, Ph.D.
> >  Dept. of Life Sciences
> >  Ben-Gurion University of the Negev
> >  Beer-Sheva 84105
> >  Israel
> >
> >  E-mail: bshaa...@bgu.ac.il
> >  Phone: 972-8-647-2220  Skype: boaz.shaanan
> >  Fax:   972-8-647-2992 or 972-8-646-1710
> >
> >   From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of
> > Bernard D Santarsiero [b...@uic.edu]
> >  Sent: Wednesday, August 27, 2014 6:12 PM
> >  To: CCP4BB@JISCMAIL.AC.UK
> >  Subject: [ccp4bb] ATP library file in REFMAC
> >
> > I recently refined a structure in CCP4/REFMAC with ATP in the
> > structure. Upon submission to Acta for publication, the wwPDB
> > validation report was run. Several things were flagged, including the
> > C4-C5 bond in the adenosine moiety as being too long. It generally
> > refines to 1.46-1.47A. The "ideal" distance in the
> > validation report is 1.38A, and the upon review of the ATP.cif file in
> > the REFMAC library, the target distance is 1.49A (and listed as a
> > double bond). Clearly 1.37-1.38A is a reasonable target value. HIC-Up
> > gives the target bond length as 1.404A.
> >   Where can I grab a revised ATP.cif file? I guess I'll need to re-refine
> > all of my structures and re-run the validation report.BTW, I also
> > looked at the PDB_REDO structure report for my structure, and can't
> > reproduce the Rcryst and Rfree values with the same model.
> >   Bernie --
>

[ccp4bb] Request for nominations

[Eric Montemayor]

The American Crystallographic Association is currently accepting nominations 
for the Margaret C. Etter Early Career Award.  This award recognizes 
outstanding achievement and exceptional potential in crystallographic research 
demonstrated by a scientist at an early stage of their independent career.  
Nominations must be received by May 25th to be considered for the 2013 award.

More information regarding the award can be found at: 
http://www.amercrystalassn.org/content/pages/main-award-descriptions

A nomination form with instructions can be found at: 
http://www.amercrystalassn.org/content/pages/main-awards-prizes

Please consider nominating an early career scientist!!

Regards,
Eric Montemayor