[ccp4bb] Äktaxpress uninet connector : Off topic

[Deepak Deepak]

Dear All,

Apologies for the off-topic post.

We recently acquired some old Äktaxpress systems and learned that they
require a specific USB to Uninet cable in order to connect to a PC. For
now, we only find it on Cytiva for 2700 USD.

Could you please guide me to some other seller that might have a similar
product for cheaper or if your lab might have a spare connector?

Kind regards,
Deepak

Here is the link from cytiva
https://www.cytivalifesciences.com/en/us/shop/chromatography/tools-and-accessories/cables/akta-usb-uninet-cable-p-05948



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Re: [ccp4bb] Phaser 2.8.3: Hendrickson-Lattman coefficients generated from dataset lacking anomalous signal

[Randy John Read]

Hi,

Hendrickson-Lattman coefficients are just a way of storing phase probability 
information, and they can come from different sources including atomic models. 
Phaser puts in HL coefficients because they could be handy under some 
circumstances for combining the phase information from experimental phasing. 
You might notice that only A and B are non-zero for the molecular replacement 
HL coefficients. That’s because the phase probability distribution is unimodal 
for calculated phases, whereas it’s generally bimodal for experimental phases 
(thus requiring more coefficients).

Best wishes,

Randy Read

> On 8 Feb 2024, at 14:32, Nitin Kulhar 
> <9dfccc771c91-dmarc-requ...@jiscmail.ac.uk> wrote:
> 
> Dear all
> 
> Is anomalous diffraction necessary for determining experimental phases and 
> the Hendrickson-Lattman coefficients (HLA, HLB, HLC, and HLD)?
> 
> MR solution from Phaser 2.8.3 (interfaced in ccp4 8.0.000 suite) seems to be 
> generating HLA/B/C/D coefficients from an x-ray diffraction dataset.
> 
> Wavelength: 
> 1.54179 Angstrom. 
> 
> Sample: 
> • 
> Protein-small molecule ligand complex crystal. 
> • No anomalous scatterer in the protein, the ligand, or the 
> crystallization condition.
> 
> Data reduction:
> Xtriage and aimless analyses did not indicate significant anomalous signal. 
> 
> I would appreciate any help in understanding the reasons for these 
> observations.
> 
> Thanks and regards
> Nitin Kulhar
> PhD student
> c/o Dr Rajakumara Eerappa
> Macromolecular Structural Biology Lab
> Department of Biotechnology
> Indian Institute of Technology Hyderabad
> Kandi, Sangareddy
> Telangana, India - 502284
> 
> Disclaimer:- This footer text is to convey that this email is sent by one of 
> the users of IITH. So, do not mark it as SPAM. 
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-
Randy J. Read
Department of Haematology, University of Cambridge
Cambridge Institute for Medical Research Tel: +44 1223 336500
The Keith Peters Building
Hills Road   E-mail: 
rj...@cam.ac.uk
Cambridge CB2 0XY, U.K.  
www-structmed.cimr.cam.ac.uk




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Re: [ccp4bb] Crystals with DNA

[Nicolas Foos]

Hello Careina,

In my hands, DNA protein complex crystals may be frustrating, because 
often we get good looking crystals which don't diffract at all and are 
actually not easy to improve.


I remember obtaining a lot of crystal looking a bit like "STOP" road 
sign (octogonal shape for one axis) which never diffracts. (Often 
containing only DNA not well organized)


So long story short, In my hand (transciption factor bound with 
homeodomain for example). I had good results with DNA sequence which 
results in hoverhangs. The idea was to bet on a "infinit" DNA helix 
which should help the packing.


I strongly encouraged you to rely on any other information  you can have 
to be sure of what is the best minimal sequence (like band shift 
assay). Also if you can purify the entire complex before crystallization 
assay (I don't know your protocol, but ideally, I would prepare the 
complex prot-DNA and put it on size exclusion).


The point is, you don't know /a priori /what kind of crystal packing you 
will have. It may be only due to protein protein contact and not related 
to the DNA directly.


Also, I often get good results with crystal growing condition containing 
MPD or PEG (makes me using PEG screen Familly as first approach).


I invite you to read the Timothy Richmond teams Papers on nucleosome 
they spend some times improving the resolution on very large complex. 
(Luger etal 1997).


There is many parameters, DNA sequence also change a bit the DNA 
geometry (look for A-tract), You may want to introduce such sequence to 
maybe improve the "rigidity".


Also if your DNA fragment are small, be careful with the temperature. 
The annealing and the DNA duplex formation is critical and you should be 
careful on your procedure.


I remember that small cation like Li, may help too.

HTH


Nicolas


On 08/02/2024 12:25, careinaedgo...@yahoo.com wrote:

 Hello all.

I am struggling to get defracting crystals with a protein DNA complex. 
The crystals are plentiful but they do not diffract. I am going back 
to the grind stone and relookong at my DNA sequence.
Is there any wisdom you could give me with regards to what works best 
with DNA in crystals?
From my reading it seems if the length is a multiple of 7 (for B DNA) 
and blunt ended, it will stretch over the length of the crystal and 
improve crystalisability. But if you want crystals that diffract 
better, you will need to play with length and even making it only one 
base longer or shorter can make a difference, even changing the 
morphology of the crystal? Longer is better than shorter, and 
overhangs are good for improving diffraction? Presumably because they 
stabilize contacts? It is expensive to synthesize a while bunch of 
sequences so I need to be strategic in my choice. Would appreciate any 
advice.

Thank you
Careina.



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--
Nicolas Foos PhD - ARISE fellow
https://orcid.org/-0003-2331-8399
   
EMBL Grenoble, McCarthy Team

71 av. des Martyrs,
38000 Grenoble FRANCE
   
+33 4 57 42 84 67




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[ccp4bb] RES: [ccp4bb] Crystals with DNA

[Rafael Marques]

Hi Careina.

The top two things that come to my mind is that you need to screen for 
different crystallization conditions and do some seeding. If your Crystal 
conditions does not diffract at all, probably it won’t.  Have you tried to 
optimize your condintion changing the pH or precipitant concentration?

Best wishes


Rafael Marques da Silva
PhD Student – Structural Biology
University of Leicester

Mestre em Física Biomolecular
Universidade de São Paulo

Bacharel em Ciências Biológicas
Universidade Federal de São Carlos

phone: +55 16 99766-0021

   "A sorte acompanha uma mente bem treinada"



De: CCP4 bulletin board  em nome de 
careinaedgo...@yahoo.com <02531c126adf-dmarc-requ...@jiscmail.ac.uk>
Enviado: Thursday, February 8, 2024 8:25:25 AM
Para: CCP4BB@JISCMAIL.AC.UK 
Assunto: [ccp4bb] Crystals with DNA

 Hello all.

I am struggling to get defracting crystals with a protein DNA complex. The 
crystals are plentiful but they do not diffract. I am going back to the grind 
stone and relookong at my DNA sequence.
Is there any wisdom you could give me with regards to what works best with DNA 
in crystals?
>From my reading it seems if the length is a multiple of 7 (for B DNA) and 
>blunt ended, it will stretch over the length of the crystal and improve 
>crystalisability. But if you want crystals that diffract better, you will need 
>to play with length and even making it only one base longer or shorter can 
>make a difference, even changing the morphology of the crystal? Longer is 
>better than shorter, and overhangs are good for improving diffraction? 
>Presumably because they stabilize contacts? It is expensive to synthesize a 
>while bunch of sequences so I need to be strategic in my choice. Would 
>appreciate any advice.
Thank you
Careina.



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[ccp4bb] Phaser 2.8.3: Hendrickson-Lattman coefficients generated from dataset lacking anomalous signal

[Nitin Kulhar]

Dear all

Is anomalous diffraction necessary for determining experimental phases and
the Hendrickson-Lattman coefficients (HLA, HLB, HLC, and HLD)?

MR solution from Phaser 2.8.3 (interfaced in ccp4 8.0.000 suite) seems to
be generating HLA/B/C/D coefficients from an x-ray diffraction dataset.

Wavelength:
1.54179 Angstrom.

Sample:

   1. Protein-small molecule ligand complex crystal.
   2. No anomalous scatterer in the protein, the ligand, or the
   crystallization condition.

Data reduction:
Xtriage and aimless analyses did not indicate significant anomalous signal.

I would appreciate any help in understanding the reasons for these
observations.

Thanks and regards
Nitin Kulhar
PhD student
c/o Dr Rajakumara Eerappa
Macromolecular Structural Biology Lab
Department of Biotechnology
Indian Institute of Technology Hyderabad
Kandi, Sangareddy
Telangana, India - 502284

-- 


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[ccp4bb] Cryo-EM Grant Program: Deadline March 31st 2024

[Nylese, Tara]

Dear Community,

You're invited to apply now to the Thermo Scientific Cryo-EM Grant 
Program
 and tell us how you plan to use cryo-EM methods to accelerate and advance your 
research. The top three recipients will receive free select Thermo Fisher 
Scientific products up to $10,000 USD. The award is open to graduate and 
post-doctoral students only.

Applications will be accepted through March 31, 2024. See details, eligible 
products and 
official
 rules to enter. No purchase is necessary to enter or win.

Tara Nylese
Market Development Manager, Americas
Life Sciences
Materials & Structural Analysis
Thermo Fisher Scientific
tara.nyl...@thermofisher.com



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[ccp4bb] Crystals with DNA

[careinaedgo...@yahoo.com]

 Hello all.
I am struggling to get defracting crystals with a protein DNA complex. The 
crystals are plentiful but they do not diffract. I am going back to the grind 
stone and relookong at my DNA sequence.Is there any wisdom you could give me 
with regards to what works best with DNA in crystals?From my reading it seems 
if the length is a multiple of 7 (for B DNA) and blunt ended, it will stretch 
over the length of the crystal and improve crystalisability. But if you want 
crystals that diffract better, you will need to play with length and even 
making it only one base longer or shorter can make a difference, even changing 
the morphology of the crystal? Longer is better than shorter, and overhangs are 
good for improving diffraction? Presumably because they stabilize contacts? It 
is expensive to synthesize a while bunch of sequences so I need to be strategic 
in my choice. Would appreciate any advice.Thank youCareina.



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[ccp4bb] Structural Biology Facility Manager vacancy at the John Innes Centre, Norwich UK

[David Lawson (JIC)]

Dear All,

We have a vacancy for a Structural Biology Facility Manager at the John Innes 
Centre.

The John Innes Centre is an independent, international centre of excellence in 
plant and microbial sciences. We nurture a creative, curiosity-led approach to 
answering important questions in bioscience, and translate that knowledge into 
societal benefits. Recent investment from the UKRI Infrastructure Fund will 
ensure the JIC's ability to contribute cutting-edge, world-leading research 
into the future, underpinned by excellent facilities. We are an equal 
opportunities employer, actively supporting inclusivity and diversity, and we 
provide support for ongoing career development.

We are looking for someone with extensive postdoctoral expertise in protein 
crystallography; experience of cryo-EM and SAXS would also be advantageous. The 
successful applicant will oversee the Facility and contribute to a wide variety 
of projects. The post holder will be expected to provide training and to ensure 
financial sustainability of the Facility though usage recharges and funding 
applications.

Closing date - 7th March 2024.
Salary - £43,550 - £54,900
Contract - indefinite, full-time

For further details, please visit our website http://jobs.jic.ac.uk or contact 
the Human Resources team on 01603 450814 or nbi.recruitm...@nbi.ac.uk quoting 
reference 1004561.

Best Wishes,

Dave Lawson

---

Prof. David M. Lawson
Department of Biochemistry and Metabolism,
John Innes Centre,
Norwich,
NR4 7UH, UK.
Tel: +44-(0)1603-450725
Web: https://www.jic.ac.uk/people/david-lawson
Email: david.law...@jic.ac.uk





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