Re: [ccp4bb] criteria to set resolution limit

2021-09-11 Thread Rajiv gandhi.s
Dear Chang,
One need to set resolution cut off, to have a meaningful data without
losing high resolution data and keeping data integrity. Some key quality
indicators like I/Sigma I,  CC 1/2 and Rpim etc., at outer most shell need
to be considered.  What was the CC 1/2 value in outer shell ?

Please refer to the below paper.
How good are my data and what is the resolution
Assessing and maximizing data quality in macromolecular crystallograph

On Sat, 11 Sep 2021, 9:52 pm Tao-Hsin Chang, 
wrote:

> Hi Farhan,
>
> It looks like that your diffraction data has an anisotropic issue and it
> leads to the issues of resolution limit, intensity, and completeness. Check
> The STARANISO Server (
> https://staraniso.globalphasing.org/cgi-bin/staraniso.cgi). It may be
> useful for your case.
>
> Best wishes,
> Tao-Hsin
>
> On Sep 11, 2021, at 11:55 AM, Syed Farhan Ali 
> wrote:
>
> Dear All,
>
> I have query regarding one of my dataset. I am running aimless by keeping
> highest resolution 1.62 A and getting  I/SigI = 2 but data completeness is
> around 22 in outermost shell. And if I am increasing the resolution cutoff
> up to 1.8 A then I/SigI is 6.2 and completeness is 82.4.
> I have attached the screenshot of the result.
> What should be the criteria to set the resolution limit?  Should I stick
> to  I/SigI  or I have to consider about the completeness of data.
> And if completeness is also a guiding factor than how much minimum
> completeness I can keep in the higher resolution shell.
>
>
>
>
>
> Regards,
> Farhan
>
>
>
>
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Re: [ccp4bb] Structural Alignment

2020-04-08 Thread Rajiv gandhi.s
UCSF chimera or chimeraX versions both could do the alignment of multiple
structures that also pop up the sequence alignment with secondary
structures highlighted in different colors through Match Maker. Up-to six
structures I have aligned.


Best regards
Rajivgandhi Sundaram.


On Wed, Apr 8, 2020, 11:09 PM Armando Albert  wrote:

> Thank you all,
> I have done it with chimera. It does structural alignment and use it as a
> template. Then, you can add sequences one after the other and align to this
> template.
> You can save this alignment in clustalw format and load it to ESPrit3 and
> do a nice picture.
> Armando
>
>
>
> El 8 abr 2020, a las 19:22, Guillaume Gaullier 
> escribió:
>
> Hi Armando,
>
> This seems doable with ChimeraX: https://www.cgl.ucsf.edu/chimerax/
>
> More specifically, its matchmaker command will align two structures and
> print the corresponding sequence alignment:
> https://www.cgl.ucsf.edu/chimerax/docs/user/commands/matchmaker.html
> You can then save the sequence alignment to a file, and use it in your
> favorite sequence alignment program along with the sequences for which you
> don’t have a structure.
>
> This is one option among many, as pretty much every structure
> visualization program can superimpose two similar structures (but I don’t
> know how many of them make it as easy to save the sequence alignment).
>
> Hope this helps,
>
> Guillaume
>
>
> On 8 Apr 2020, at 19:04, Armando Albert  wrote:
>
> Dear all,
> I want to align two structures and then, I want to align several sequences
> to that structural alignment.
> How can I do this?
> Armando
>
> 
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Re: [ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] on-topic: your opinions requested!

2020-04-07 Thread Rajiv gandhi.s
Any paper published should share the data publicly, it is the job of the
journal editor to ask so. If they don't want to disclose to scientific
community then, how one could trust the data  published in that paper
describes active site and key structural information. Contact the editor of
the journal, that's ideal.

On Tue, Apr 7, 2020, 10:41 PM Frank von Delft 
wrote:

> I meant:  complain to the editor for accepting a paper without released
> coordinates.  We as a community fought and won that battle >20 years ago -
> so we have the weight of history on our side.
>
>
> On 07/04/2020 17:05, Schreuder, Herman /DE wrote:
>
> Dear Frank,
>
>
>
> here I disagree. I think it is bad practice to complain to the editors or
> start naming and shaming before asking the authors first. Only if they do
> not want to cooperate, it would be time to bring the flame-throwers in
> position.
>
>
>
> However, I think the situation is more subtle and that that is the reason
> Artem wrote his email: He wants the data, but does not want to reveal his
> identity to his competitors, who apparently made a significant effort not
> to reveal any useful details.
>
>
>
> Here I would let me guide by the (perceived) commercial interest: if it is
> not gigantic, then I would contact the authors to prevent a wasteful
> duplication of research efforts.
>
> If there is a significant commercial interest, it would probably be better
> not to contact them and go the hard way of solving the structure yourself.
> A thing to consider is also what would happen if the authors still would
> refuse: they know the identity of the competitor and you still do not have
> the data.
>
>
>
> An alternative may be to ask an academic friend who also works on sausage
> esterases to inquire with the authors…
>
>
>
> Good luck with your decision!
>
> Herman
>
>
>
> *Von:* CCP4 bulletin board   *Im
> Auftrag von *Frank von Delft
> *Gesendet:* Dienstag, 7. April 2020 17:19
> *An:* CCP4BB@JISCMAIL.AC.UK
> *Betreff:* [EXTERNAL] Re: [ccp4bb] on-topic: your opinions requested!
>
>
>
> *EXTERNAL : *Real sender is owner-ccp...@jiscmail.ac.uk
>
>
>
> Write to the editor - that's their job.
>
> Though they may also see it as their job to ignore emails like yours
> because that's far easier than dealing with them.
>
> Alternatively, go the Rupp Route:  Name and Shame! ;)
>
> On 07/04/2020 16:08, Artem Evdokimov wrote:
>
> Dear CCP4ers,
>
>
>
> I would like to solicit your thoughts on the following (this is a real
> situation, but salient details are changed):
>
>
>
> Imagine that you're an industrial scientist in a small company, working on
> the Bavarian Sausage (Weisswurst) Esterase project. The overall structure
> is previously unknown, with no good homologs in the PDB, trying to model
> is "OK not great" so the structure is really needed...
>
>
>
> Then, you find an article from a large commercial competitor, that somehow
> managed to solve the Stadtwurst (Saxony Sausage) Esterase structure (which
> is a very close homolog to the one you need!).
>
>
>
> Sounds good - but as you read the paper you realize that the authors
> managed to find a journal that allowed them to publish their work without
> disclosing neither the coordinates of the model, nor even the
> crystallization conditions of the protein - all that's available is a
> tantalizing still picture of the active site in surface mode, with a
> ball-and-stick ligand positioned such that it is impossible to say what it
> interacts with.
>
>
>
> So you sit and ponder - whether to write to the Editor, or maybe to
> contact the authors directly (but then they would know that you're working
> on this, which is not necessarily great since you're competing), or to just
> buck up and do the structure on your own (which feels a bit wasteful).
> Then, you realize that your friends at CCP4 have a lot of wisdom to offer,
> so you sit down and pen an email...
>
>
>
> Any thoughts?
>
>
>
> Artem
>
>
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Re: [ccp4bb] Crystal screen for DNA binding proteins

2019-10-15 Thread Rajiv gandhi.s
This following screen Is generally used for DNA but one can give a try for
dna-protein complex as well.


https://hamptonresearch.com/product-Individual-Natrix-Natrix-2-Natrix-HT-Reagents-512.html

https://www.jenabioscience.com/crystallography-cryo-em/screening/crystal-screens/jbscreen-nuc-pro

Best regards
Rajiv

On Tue, Oct 15, 2019, 1:19 PM Sylvia Fanucchi 
wrote:

>
>
> Hi
>
> Can anyone recommend a good crystal screen to use to crystalise protein-NA
> complexes?
>
>
>
> Kind Regards
>
> Sylvia
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Re: [ccp4bb] ITC question -dimer vs monomer

2019-10-03 Thread Rajiv gandhi.s
Dear Dr.BR

There could be two possibilities,  you could try to do titration of dimer
into monomer loaded in cell or vice versa, and with subtraction of heat of
dilution from protein-protein titration. These kind of molecular
interaction involving distinct oligomer units need be addressed  by any
other orthogonal methods.

Regards
Rajivgandhi Sundaram


On Thu, Oct 3, 2019, 10:21 PM clare stevenson (JIC) <
clare.steven...@jic.ac.uk> wrote:

> I would try it both ways and see what you get.  Also do controls of buffer
> into each protein
>
>
>
> For extra info could also try with SPR.  Always best to do these things
> using multiple complimentary methods
>
>
>
> Best wishes
>
>
>
> Clare
>
>
>
> *From:* CCP4 bulletin board  *On Behalf Of *Bernhard
> Rupp
> *Sent:* 03 October 2019 16:06
> *To:* CCP4BB@JISCMAIL.AC.UK
> *Subject:* [ccp4bb] ITC question -dimer vs monomer
>
>
>
> Hi Fellows,
>
>
>
> please let me ask the respective experts an ITC question: I have 2
> proteins, stable and dialyzed in identical buffer.
>
> A is a monomer and B an obligate dimer. I suspect that eventually a A2B2
> dimer will form.
>
>
>
> Intuitively, it should make a difference whether I titrate the dimer with
> the monomer or vice versa.
>
> In the first case, a momomer would initially meet a lot of free dimers,
> and I would expect that randomly, a AB2 complex
>
> is more likely to form than a A2B2 (let’s disregard any more complex
> colligative/cooperative effects).
>
>
>
> If I drip the dimer into the monomer pool, it is quite likely that the B
> dimer meets 2 free As, and I get right away a higher population of A2B2s.
>
>
>
> Maybe at dilutions of ITC and with sufficient equilibration that is not an
> issue at all (again, absent any cooperative effects that might alter the
> first Kd vs. the second, despite the sites on the dimer are at least
> initially equivalent).
>
>
>
> Can someone guide me towards literature about this or perhaps share some
> first-hand experience?
>
>
>
> Many thanks, BR
>
>
>
> --
>
> Bernhard Rupp
>
> http://www.hofkristallamt.org/
>
> b...@hofkristallamt.org
>
> +1 925 209 7429
>
> +43 676 571 0536
>
> --
>
> Many plausible ideas vanish
>
> at the presence of thought
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Re: [ccp4bb] Reg: water pentagon at dimer interface

2019-09-27 Thread Rajiv gandhi.s
There are literature shown this kind of  possiblity to have dimerization
via water mediated interactions. But look whether in solution also they
could form dimer or not.  How to figure out it is not non specific, it is
physiological relevant.

Cheers
SR

On Fri, Sep 27, 2019, 5:04 PM Vijaykumar Pillalamarri <
vijaypkuma...@gmail.com> wrote:

> Dear Community,
>
> I solved the structure of a protein from vibrio. There are two
> molecules in the asymmetric unit of this protein. At the dimer interface,
> the C-termini of both the chains interact with each other with the help of
> five water molecules that form a pentagon. I have attached an image showing
> both the chains and stereo image of dimer interface in the inset. I was
> wondering if there is any significance to this or if there is any relevant
> literature that explains this behavior.
>
> Thank you
> Vijaykumar Pillalamarri
> C/O: Dr. Anthony Addlagatta
> Principal Scientist
> CSIR-IICT, Tarnaka
> Hyderabad, India-57
> Mobile: +918886922975
>
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Re: [ccp4bb] Optimization from needle shaped crystals

2019-09-08 Thread Rajiv gandhi.s
Dear prem,
I am sharing my experience with needle crystal that worked for me.

1.First check that salt or  a protein crystal by SDS PAGE or mass
spectroscopy.
2. For improvement of morphology and size,  you could try microseeding of
your crushed crystal, generally needle crystal appear quickly, further this
could be improved by seeding them again in 96 well plates with commercial
screens. If this yield any improved crystals then Pick the best looking and
larger sized crystal to seed again into 24 well plates, by streaking the
seed solution using cat whisker.

3. If you get any better crystal from seeding, then do a grid screening
around the original condition.

4. Try to do different volume ratios of protein with well solution, and
even keep them at cold room. Also you could vary the protein concentration.

5. Do an additive screen as well, once you figure out  condition that yield
better crystal morphology and with improved  thickness.

Hope this helps

Best

Rajivgandhi Sundaram
Macromolecular crystallography lab
institute of life Sciences
India.

On Sun, Sep 8, 2019, 10:10 AM Prem Prakash  wrote:

> Dear all,
> Sorry for a trivial query. I am trying to Co-crystallize my protein with
> its substrate (peptide) using commercial screenings. In one condition of
> JCSG plus (Molecular Dimension) that contains  0.2 M Magnesium chloride
> hexahydrate,  0.1 M Tris 8.5 50 % v/v Ethylene glycol, I got needle like
> crystals (picture attached). Does anyone have idea to optimize such needles
> into better crystals. I would appreciate all your suggestions.
>
> Thank you
> With kind regards,
> Prem Prakash  (Ph.D.)
>
>
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Re: [ccp4bb] SEC and MALS

2019-08-27 Thread Rajiv gandhi.s
Because MALS can capture distinct migrant form of the same protein,
sometimes  protein with disorder and elongated structure behave differently
in  SEC. In SEC we can't distinguish them.  Whereas MALS have scattering at
three different angles,  by that we can captures those multiple forms of
the same protein.
Please provide the image for more information.

On Tue, Aug 27, 2019, 12:30 PM Petri Kursula 
wrote:

> Hi,
> that's typical behaviour for an elongated/disordered molecule, given that
> SEC separates based on hydrodynamic radius, not MW.
> Petri
>
> Petri Kursula
> --
> Professor
> --
> Department of Biomedicine
> University of Bergen, Norway
> http://www.uib.no/en/rg/petrikursula
> 
> petri.kurs...@uib.no 
> --
> Faculty of Biochemistry and Molecular Medicine
> University of Oulu, Finland
> --
>
>
>
>
>
>
> On 27 Aug 2019, at 07:57, Natesh Ramanathan  > wrote:
>
> Dear  Friends,
>
> Can you share your experience with examples of MALS giving lower
> molecular weight (Eg. Monomer) and  SEC giving higher molecular weight (Eg.
> Dimer),  for the same protein sample?
>
>   If you have/know any published paper, can you please point me to
> that reference paper or send me the paper?
>
> Many thanks.
> Best regards,
> Natesh
>
>
> --
> --
> "Live Simply and do Serious Things .. "
> - Dorothy Mary Crowfoot Hodgkin OM, FRS
>
> "In Science truth always wins"
> - Max Ferdinand Perutz OM FRS
> --
> Dr. Ramanathan Natesh
> Assistant Professor,
> School of Biology,
> Indian Institute of Science Education and Research Thiruvananthapuram
> (IISER-TVM),
> Maruthamala P.O., Vithura,
> Thiruvananthapuram,  695551, Kerala, India
>
> nat...@iisertvm.ac.in
> http://www.researcherid.com/rid/C-4488-2008
> ORCID: http://orcid.org/-0002-1145-5962
> https://publons.com/author/1520837/ramanathan-natesh#profile
> http://faculty.iisertvm.ac.in/natesh
>
> Office Ph. 0091- 471-2778087
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