[ccp4bb] Brazil offers oportunities for researchers from countries involved in war-affected countries

[Maria Cristina Nonato]

Please have a look at:
https://fapesp.br/15402/initiative-researchers-at-risk.

Best regards

Cristy


-- 

*Cristina Nonato, Cristy, Cris, Cristininha*

Associate III Professor
Laboratório de Cristalografia de Proteínas
Faculdade de Ciências Farmacêuticas de Ribeirão Preto - USP



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[ccp4bb] Should Rmerge be reported?

[Maria Cristina Nonato]

Dear Colleagues
Hope to find you all well and healthy.

I have a question regarding Rmerge. In recent years, we have published our
crystallographic structures in highly respected journals using CC1/2,
I/sigma(I), completeness and multiplicity as quality parameters for our
diffraction data.

Recently this year, We submitted a paper using the same strategy, but one
of the reviewers asked us to provide the Rmerge, arguing that providing
this data was compulsory and it was important to estimate radiation damage.

We replied to the editor arguing that Rmerge should not be used as a
quality parameter, as suggested by more recent literature, such as the
article published by Karplus and Diederichs (10.1016/j.sbi.2015.07.003). We
also argued that there are modern and efficient methods to estimate
radiation damage ( doi.org/10.1107/S1600576718005241;
doi.org/10.1107/S0907444909040177). It is my opinion that an experienced
crystallographer can even  monitor radiation damage over the course of data
processing.

And our paper was rejected  due to the fact I did not
provide Rmerge which I certainly could have done If I found necessary.

Journals like Nature ((https://www.nature.com › documents › nr-tables-xray

) and even IUCr Journals (
https://journals.iucr.org/f/services/structuralcommunications/) still list
Rmerge as a data to be reported. I always took this as a suggestion since
there are people still using Rmerge for data cutoff, but I never took this
as if Rmerge was a compulsory data to be reported.

I would like to hear the opinion of this community. Should we compulsorily
report Rmerge?  If so, Why?

Cheers,

Cristy
-- 

*Cristina Nonato*
Associate Professor
Laboratório de Cristalografia de Proteínas
Faculdade de Ciências Farmacêuticas de Ribeirão Preto
University of São Paulo



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Re: [ccp4bb] Co-crystallization and thermal shift assay

[Maria Cristina Nonato]

*Dear Saif*

*Hope you are doing well and safe!*

1) How much change in Tm (ΔTm) in a thermal shift assay is considered to be
significant ?

*As it has already been mentioned there is no specific cutoff  for deltaTm
to be considered significant. DeltaTm depends on many factors, including
the type of dye you use, protein structure and where your compound binds*.

2) A negative  ΔTm infers that the compound is making the protein unstable.
In such a case, will the co-crystallization be difficult or just impossible
or on the contrary it shouldn't matter much?


*A negative detaTm means the compound is binding to a different
conformational state of the protein, compared to the native one. I would
not consider co-crystallization more difficult or impossible in the
presence of those compounds, but I would definitely screen for different
crystallization conditions.*

*Good luck*

*Cristy*
*#womeninscience*


Em qui., 25 de fev. de 2021 às 11:56, Saif Mohd 
escreveu:

> Hello everyone,
>
> 1) How much change in Tm (ΔTm) in a thermal shift assay is considered to
> be significant ?
>
> 2) A negative  ΔTm infers that the compound is making the protein
> unstable. In such a case, will the co-crystallization be difficult or just
> impossible or on the contrary it shouldn't matter much?
>
>
> Thanks and best regards,
> Saif
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>



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[ccp4bb]

[Maria Cristina Nonato]

Dear Changyi

I do not know details about your structure, but considering you have the 
correct library for your ligand and your resolution is not bad, I would check a 
possible double conformation.
Good luck
Cristy

On Wed, 4 Aug 2010 16:15:55 -0400, Changyi Xue wrote
 Dear all, 
 
   In my structure, there is a ligand, whichcontains a sugar ring. In the 
 process of refinement, refmac alwaystried to distort the sugar ring to fit 
 into the density. Is there anyway to fix or restrain the ring conformation 
 more tightly? I know CNShas such function, just wandering if refmac could do 
 it also. 
 
   all suggestions are welcome.
 
 changyi

- 
Profa Dra Maria Cristina Nonato 
Laboratório de Cristalografia de Proteínas 
Departamento de Física e Química 
Faculdade de Ciências Farmacêuticas de Ribeirão Preto - USP 
Fone: +55.16.3602.4432  Fax: +55.16.3602.4880 
cri...@fcfrp.usp.br