Re: [ccp4bb] [6HR5] collected on an Eiger so Rmerge not relevant

[Kay Diederichs]

First of all, you are of course correct, Rmerge (as Rmeas, Rpim, CC1/2, I/sigma 
...) is not detector-dependent. 

Second, when looking at the "experiment" section of the PDB deposition, I note 
that some Rmerge values are even given there! The statistics there are dubious, 
e.g. seemingly the I/sigma in the high resolution shell is 2.2 meaning that 
they could have used higher resolution data.

Third, look at the sliders on the entry page: the validity of this PDB entry is 
suspicious - quite bad Rfree and geometry.

One more case for the deposition of raw data. In my eyes, the RCSB policy 
should be that raw data must be deposited when accepting such a bad entry.

HTH,
Kay

On Wed, 31 Jul 2019 17:49:47 +0100, Weston Lane  wrote:

>I was looking at the following structure in the PDB:  
>http://www.rcsb.org/structure/6HR5  I noticed that the R/Rfree stats were 
>pretty high for 2.9A resolution so I followed up by looking for the "Table 1" 
>statistics in the journal article.   Link to article: 
>https://www.nature.com/articles/s41589-019-0311-9  Table is located in the 
>supplemental materials "Table 9".
>
>From the processing statistics it's clear that the diffraction from that 
>crystal wasn't great but I don't want to get hung up on the processing or the 
>validity of the structure.  What struck me what this little explanation the 
>authors included to explain the outlier statistics in the table:
>
>"Crystal of P36_S1_25 was collected on an Eiger detector, so Rmerge data are 
>not relevant."
>
>We all know that Rmerge isn't a great metric for data quality but I've never 
>heard that it's detector-dependent.  This doesn't make sense to me.  If it's 
>actually true can someone explain, please?
>
>Thanks!
>
>Wes
>
>
>
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Re: [ccp4bb] [EXTERNAL] [ccp4bb] [6HR5] collected on an Eiger so Rmerge not relevant

[Ivan Shabalin]

Hi Clemens,

I fully agree with you, especially on overall data collection strategy 
and on image deposition.


It looks like an interesting and mysterious case. Mean I Over Sigma is 
reported as 2.2 - I'm curious why resolution was not extend. Since they 
disregarded Rmerge (a reasonable thing to do, as pointed by others), it 
in not clear to me why not to extend. And Rfree of 36% seems really high.


Ivan

With best regards,
Ivan Shabalin, Ph.D.
Research Scientist,
Department of Molecular Physiology and Biological Physics,
University of Virginia,
1340 Jefferson Park Avenue, Pinn Hall,Room 4223,
Charlottesville, VA 22908
https://www.linkedin.com/in/shabalinig/
https://minorlab.org/person/ivan_s/

On 7/31/19 17:16, Clemens Vonrhein wrote:

Hi,

On Wed, Jul 31, 2019 at 07:11:10PM +0100, Weston Lane wrote:

Thanks for the response. I did look at the multiplicity of the
datasets in their table and while I suppose 6.9x redundancy is sort
of high for P2 spacegroup it's actually lower than some of the other
datasets (presumably non-Eiger) in the table with good overall
Rmerge (e.g. a C2 dataset with 10x redundancy and an Rmerge of
0.064).


Maybe a multiplicity of 6.9 is not especially low for monoclinic: 5LP9
for example (Pilatus data) has 6.3 for 360 degree of data (and Rmerge
of 0.045 to 0.864A when re-processing). Yes, that is more data than
traditionally collected for monoclinic (180 degree), but still far
away from some real high multiplicity approaches.

So this looks much more like a crysal issue to me: maybe there are
some really poor image ranges (that then give an overall Rmerge of
0.256). The overall I/sigI is also rather low (7), and if you look at

   http://staraniso.globalphasing.org/cgi-bin/PDBpeep.cgi?ID=6hr5

you can see that even in the lowest shell the I/sigI is only about
15 - so maybe a seriously underexposed crystal?

Low dose, high-multiplicity is very good - but only if one still takes
advantage of the dose budget a crystal provides. It doesn't help
underexposing a crystal for only 360 degree if it could give still
good data for 720, 1080 or 1440 degree. The great opportunity of low
dose, high multiplicity is that it allows one to see radiation damage
happening and then selecting a subset of images from the start that
are still complete with a nice multiplicity.

At least that is how I approach this with Pilatus/Eiger detectors (or
other photon counting ones) ...

Cheers

Clemens

PS: it would be great to have those images deposited (at
 proteindiffraction.org, sbgrid,org or zenodo.org et al) :-)







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Re: [ccp4bb] [EXTERNAL] [ccp4bb] [6HR5] collected on an Eiger so Rmerge not relevant

[Clemens Vonrhein]

Hi,

On Wed, Jul 31, 2019 at 07:11:10PM +0100, Weston Lane wrote:
> Thanks for the response. I did look at the multiplicity of the
> datasets in their table and while I suppose 6.9x redundancy is sort
> of high for P2 spacegroup it's actually lower than some of the other
> datasets (presumably non-Eiger) in the table with good overall
> Rmerge (e.g. a C2 dataset with 10x redundancy and an Rmerge of
> 0.064).

Maybe a multiplicity of 6.9 is not especially low for monoclinic: 5LP9
for example (Pilatus data) has 6.3 for 360 degree of data (and Rmerge
of 0.045 to 0.864A when re-processing). Yes, that is more data than
traditionally collected for monoclinic (180 degree), but still far
away from some real high multiplicity approaches.

So this looks much more like a crysal issue to me: maybe there are
some really poor image ranges (that then give an overall Rmerge of
0.256). The overall I/sigI is also rather low (7), and if you look at

  http://staraniso.globalphasing.org/cgi-bin/PDBpeep.cgi?ID=6hr5

you can see that even in the lowest shell the I/sigI is only about
15 - so maybe a seriously underexposed crystal?

Low dose, high-multiplicity is very good - but only if one still takes
advantage of the dose budget a crystal provides. It doesn't help
underexposing a crystal for only 360 degree if it could give still
good data for 720, 1080 or 1440 degree. The great opportunity of low
dose, high multiplicity is that it allows one to see radiation damage
happening and then selecting a subset of images from the start that
are still complete with a nice multiplicity.

At least that is how I approach this with Pilatus/Eiger detectors (or
other photon counting ones) ...

Cheers

Clemens

PS: it would be great to have those images deposited (at
proteindiffraction.org, sbgrid,org or zenodo.org et al) :-)

-- 

*--
* Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com
* Global Phasing Ltd., Sheraton House, Castle Park 
* Cambridge CB3 0AX, UK   www.globalphasing.com
*--



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[ccp4bb] RESEARCH SCIENTIST POSITION in INSTITUTE FOR PROTEIN DESIGN

[StrBio]

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Department: BIOCHEMISTRY - INSTITUTE FOR PROTEIN DESIGN
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The UW Institute for Protein Design is seeking to hire a *RESEARCH
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[ccp4bb] Postdoctoral Position Available at Rutgers University

[Matthew Neiditch]

An NIH-funded postdoctoral position is available at Rutgers University - New 
Jersey Medical School to study the structural basis of bacterial competence, 
more specifically the movement of DNA across bacterial membranes during natural 
transformation. In addition to a recent Ph.D., the ideal candidate will have a 
strong background in macromolecular X-ray crystallography, cryoEM, 
biochemistry, protein purification, and molecular biology. A working knowledge 
of bacterial genetics is a plus. Candidates with demonstrated success in 
another field and a strong commitment to learning X-ray crystallography and 
cryoEM will also be considered. Please submit: CV and at least 2 letters of 
reference to matthew.neidi...@rutgers.edu and dubna...@njms.rutgers.edu with 
the subject line Postdoctoral Position Applicant.

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Associate Professor
Dept. of Microbiology and Molecular Genetics
New Jersey Medical School
Rutgers University

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Professor
Public Health Research Institute
New Jersey Medical School
Rutgers University



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Re: [ccp4bb] [EXTERNAL] [ccp4bb] [6HR5] collected on an Eiger so Rmerge not relevant

[Weston Lane]

Edward,

Thanks for the response. I did look at the multiplicity of the datasets in 
their table and while I suppose 6.9x redundancy is sort of high for P2 
spacegroup it's actually lower than some of the other datasets (presumably 
non-Eiger) in the table with good overall Rmerge (e.g. a C2 dataset with 10x 
redundancy and an Rmerge of 0.064).

W



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Re: [ccp4bb] [EXTERNAL] [ccp4bb] [6HR5] collected on an Eiger so Rmerge not relevant

[Edward A. Berry]

I think it is not really the detector, but the strategy. If you decrease 
exposure time by a factor of ten and make up for it by 10 x higher redundancy, 
then obviously R-merge, which is a measure of accuracy of the individual 
frames, is going to suffer. Chi^2 statistics can distinguish this from a real 
problem with the data reduction. And I guess the capabilities of the Eiger 
detectors tend to encourage high-redundancy, low dose/frame strategies? (No 
6HR5 is not mine).

On 07/31/2019 12:49 PM, Weston Lane wrote:

I was looking at the following structure in the PDB:  
https://urldefense.proofpoint.com/v2/url?u=http-3A__www.rcsb.org_structure_6HR5=DwIFaQ=ogn2iPkgF7TkVSicOVBfKg=cFgyH4s-peZ6Pfyh0zB379rxK2XG5oHu7VblrALfYPA=2NZPl2iBIAyGDtZO7h2CtE0DqQqnPQb_sHo94gbPGAo=yti3AVLhix2oCPzcWyto9IuLqgqbU7KWxfTgQ0hleBY=
   I noticed that the R/Rfree stats were pretty high for 2.9A resolution so I followed up by looking for the "Table 1" statistics in the 
journal article.   Link to article: 
https://urldefense.proofpoint.com/v2/url?u=https-3A__www.nature.com_articles_s41589-2D019-2D0311-2D9=DwIFaQ=ogn2iPkgF7TkVSicOVBfKg=cFgyH4s-peZ6Pfyh0zB379rxK2XG5oHu7VblrALfYPA=2NZPl2iBIAyGDtZO7h2CtE0DqQqnPQb_sHo94gbPGAo=qkFehKN3fqEKQJMkmTiecg_OMR82xFIi_5h8yCl-AZs=
   Table is located in the supplemental materials "Table 9".

 From the processing statistics it's clear that the diffraction from that 
crystal wasn't great but I don't want to get hung up on the processing or the 
validity of the structure.  What struck me what this little explanation the 
authors included to explain the outlier statistics in the table:

"Crystal of P36_S1_25 was collected on an Eiger detector, so Rmerge data are not 
relevant."

We all know that Rmerge isn't a great metric for data quality but I've never 
heard that it's detector-dependent.  This doesn't make sense to me.  If it's 
actually true can someone explain, please?

Thanks!

Wes



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[ccp4bb] [6HR5] collected on an Eiger so Rmerge not relevant

[Weston Lane]

I was looking at the following structure in the PDB:  
http://www.rcsb.org/structure/6HR5  I noticed that the R/Rfree stats were 
pretty high for 2.9A resolution so I followed up by looking for the "Table 1" 
statistics in the journal article.   Link to article: 
https://www.nature.com/articles/s41589-019-0311-9  Table is located in the 
supplemental materials "Table 9".

From the processing statistics it's clear that the diffraction from that 
crystal wasn't great but I don't want to get hung up on the processing or the 
validity of the structure.  What struck me what this little explanation the 
authors included to explain the outlier statistics in the table:

"Crystal of P36_S1_25 was collected on an Eiger detector, so Rmerge data are 
not relevant."

We all know that Rmerge isn't a great metric for data quality but I've never 
heard that it's detector-dependent.  This doesn't make sense to me.  If it's 
actually true can someone explain, please?

Thanks!

Wes



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[ccp4bb] Conference in Rome on CryoElectron Microscopy in Structural Biology, 10-11 October 2019

[Adriana E. Miele]

Dear CCP4BBoarders,

on behalf of the Organizing committee we would like to invite you to the Conference “CryoElectron Microscopy in Structural Biology: paving the way towards biomedicine and biotechnology”, jointly organised by Sapienza University of Rome and CNR Institute of Molecular Biology and Pathology to remember the pioneering work of late Prof Emilia Chiancone. 
International scientists will be presenting the ensemble of their breakthrough research, among them Prof. Ben Luisi, who will give an EMBO Keynote Lecture.
A round table on the importance of developing infrastructures and networking will close the event, which will take place in Rome 10th - 11th October 2019. 
Bursaries for young scientists are available from SIB (Società Italiana di Biochimica e Biologia Molecolare) and AIC (Associazione Italiana di Cristallografia).

More info and the detailed programme at : 
https://prometeus-rise.org/10th-11th-october-2019-cryo-electron-microscopy-in-structural-biology-a-conference-in-memory-of-emilia-chiancone/

The deadline for registration is on September 15th 2019.
Due to conference venue size, the attendance will be limited to 100 people, on a first-come first-served base.

Best regards,
Adriana Erica Miele & the Organising Committee
Francesco Angelucci, Giovanna Boumis, Adele Di Matteo, Cécile Exertier, Luca Federici, Annarita Fiorillo, Giorgio Giardina, Andrea Ilari, Linda Celeste Montemiglio, Linda Savino, Beatrice Vallone


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