Re: [ccp4bb] Off-topic, protein in dye-front (ion front?) on native-PAGE

[Xiao Lei]

Hi All,

Sorry to bring this old topic up again.  I planned to run tricine gels but
I found a possible error in table 2 (4% stacking gel formula) in Hermann
Schägger protocol (Nature Protocols volume 1, pages 16–22 (2006), the
author wrote 3ml 3X gel buffer in a total of 12 ml solution, it should be
4ml 3X gel buffer in a total of 12 ml solution right?

I tried to contact the author but unsuccessful, I do not know if anyone in
this forum has noticed if this is an error or not.

Xiao


On Thu, Jan 19, 2017 at 8:00 AM Didier Spittler 
wrote:

> Yes Tris-Tricine gel !
>
> Try to obtain this article from nature protocol.
>
> Best,
>
> Didier
>
>
> 2017-01-19 14:47 GMT+01:00 zeyaul islam :
>
>> Try Tricine gel. It is particularly suited for low molecular wt proteins
>> and it will give you very good resolution. Even you can run it overnight at
>> 30 V (16-18 hours).
>>
>> On Thu, Jan 19, 2017 at 9:33 AM, Walt  wrote:
>>
>>> Hi,
>>>
>>> I have a small protein (~9 kDa) with acidic pI (~4).
>>> When I run 18% native-PAGE, it appears my protein is in the dye front.
>>> How can I fix this problem? Changing the pH of separating gel
>>> might help? How about gradient native-PAGE? Thank you!
>>>
>>> Walt
>>>
>>
>>
>
>
> --
> Didier Spittler, PhD
> Phone number : +33658576481
>



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[ccp4bb] PDRA Position, Leicester, with Peter Moody

[Peter Moody]

I have a BBSRC-funded PDRA position for someone to come and work with me at
the Leicester Institute for Structural & Chemical Biology, and so  this is
about to be posted on jobs.ac.uk.   Please contact me using my university
email, and not through this account (as the message will probaly get lost).
Vacancy Name: Postdoctoral Research Associate
Vacancy ID: 474
Vacancy Department: Leicester Institute of Structural and Chemical
Biology/Molecular and Cell Biology
Advertising Start Date: 28/09/2018 00:00:00
Advertised Salary: Grade 7 £34,189 to £39,609 per annum


We wish to recruit a Postdoctoral Researcher to the group of Prof Peter
Moody to take a leading role in a programme of research to investigate the
mechanism of heme peroxidases, using advanced and innovative structural and
spectroscopic methods. Our work is summarised in Moody & Raven (2018)
*Acc.Chem.
Res.* 51 (2), pp 427–435 *DOI: *10.1021/acs.accounts.7b00463, and in more
detail in the papers listed on Peter Moody’s Departmental home page https
://www2.le.ac.uk/departments/molcellbiol/staff/moody


The research is funded by the BBSRC and is a collaboration with Professor
Emma Raven of the Chemistry Department at Bristol University (http://www.
bris.ac.uk/chemistry/people/emma-raven/index.html) and will involve
expressing and purifying proteins from recombinant sources, gaining s
tructural and mechanistic insights using X-ray (using home and synchrotron
sources) and Neutron crystallography (using ILL Grenoble, FRM-II Munich and
ONRL, USA). We have recently conducted experiments using the Free Electron
Laser SACLA in Japan and hope to use other FEL sources such as EuXFEL soon.
Leicester has recently acquired state of the art cryo-electron microscopes
and we would like to explore the potential for micro electron diffraction.
A wide range of biochemical and biophysical techniques (especially
spectroscopy) will be used to explore enzyme intermediates.

You will  develop your own original research projects, in line with the
aims and objectives of the research programme and assist with the
supervision of graduate and undergraduate students. You will write up your
research findings for dissemination amongst the research team and the
broader international community and make presentations at scientific
meetings in the UK and overseas.
About you

The successful applicant should hold a PhD, have a strong background in
biochemical or structural analysis of proteins and have a keen interest in
experimental design and determining the direction of the research programme.

Additional information

LISCB comprises over 20 research groups drawn from several departments,
including the Department of Molecular and Cell Biology, and brings together
internationally renowned research using structural biology, chemical
biology and single molecule methods to investigate major challenges in
fundamental biological processes into a single world-leading unit.

The University of Leicester is committed to international excellence,
world-changing research and high quality, inspirational teaching. Recently,
the MRC in partnership with the Universities of Leicester, Warwick,
Nottingham and Birmingham has invested into a state-of-the-art CryoEM
facility at the Leicester Institute for Structural and Chemical Biology (
LISCB), one of four new, flagship Research Institutes of the University of
Leicester. We are strongly committed to inclusivity, promoting equality and
celebrating diversity among our staff and students. You will develop your
career in a supportive and collaborative academic environment in one of the
world’s leading research-intensive universities; elite in the excellence of
our research, yet distinctive for the genuine synergy between our research
and teaching.
In return for your hard work, we offer a working environment that is
committed to inclusivity, through promoting equality and valuing diversity.
We offer a salary package with excellent pension scheme, a generous annual
leave allowance and an online portal that offers a range of lifestyle
benefits and discounts. Located close to Leicester city centre, our award
winning campus benefits from a wide range of cafes, a fully equipped sports
centre and nursery facilities. Further information regarding our extensive
range of staff benefits is available here.



Informal enquiries and are welcome and should be made to Professor Peter
Moody on Tel: +44 (0)116 229 7097 or email: peter.mo...@leicester.ac.uk




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Re: [ccp4bb] R-merge is too high !!

[Rajesh Kumar]

I totally agree with Berry. Please consider Rpim, CC1/2 and I/sigI for
cutting the data. Rmerge is old approach as it is data redundancy dependent.

Thank you
Rajesh

---x
With regards
Rajesh K. Harijan, Ph.D.
Schramm Laboratory
Albert Einstein College of Medicine
1300 Morris Park Ave., Bronx, NY 10461
Tel: 718.430.2777  |  Fax: 718.430.8565


On Fri, Sep 28, 2018 at 11:32 AM Edward A. Berry  wrote:

> The fact that chi^2 is approximately 1.0 in all shells says that the
> deviations are about what is expected from the error model. The fact that
> Rpim is much lower than Rmeas means that you have rather high redundancy.
> This would seem to be a case of collecting low dose per image and making up
> for it with high redundancy, a strategy that has been recommended to ensure
> a full dataset even in the case of high radiation sensitivity.  In my
> opinion the high Rmerge is nothing to worry about. Look instead at CC1/2
> and I/sigI which seem fine.
>
> On 09/28/2018 04:09 AM, Zhang Foggy wrote:
> > Dear All,
> >
> > Sorry for the off-topic.
> >
> > I recently collected a set of data. The diffraction spots are extremely
> sharp. However, When I used HKL3000 to scale it, I get a final resolution
> at 3.1A with overall R-merge ~0.54 (R-merge in the highest 3.2A-3.1A shell:
> 1.59). Then I solve the structure with final R value 0.19 and R free value
> 0.24 although I know this Rmerge value is totally unacceptable, and the
> density looks perfect.
> >
> > I also tried to collect other four set of data with different crystals.
> unfortunately, all of them have same problem.
> >
> > I ask one of my friend who is an expert in HKL3000, but he had no idea
> about it. Does anyone has suggestions?
> >
> > Here is the scale information for your review:
> > Space group: P43 (I also tried P1, the Rmerge value is still similar)
> >
> > Shell Lower Upper Average  Average Norm. Linear Square
> >   limitAngstrom   I   error   stat. Chi**2  R-fac  R-fac  Rmeas
>  Rpim  CC1/2CC*
> >50.00   6.6711.6 0.9 0.3  1.165  0.191  0.284  0.198
> 0.052  0.975  0.994
> > 6.67   5.30 4.5 0.5 0.3  0.952  0.317  0.313  0.329
> 0.086  0.971  0.993
> > 5.30   4.63 7.3 0.7 0.5  0.961  0.293  0.297  0.304
> 0.081  0.975  0.994
> > 4.63   4.21 7.0 0.8 0.6  0.986  0.369  0.358  0.382
> 0.101  0.969  0.992
> > 4.21   3.91 5.6 0.8 0.6  1.040  0.522  0.491  0.541
> 0.142  0.955  0.988
> > 3.91   3.68 4.6 0.9 0.7  1.064  0.718  0.669  0.746
> 0.203  0.929  0.981
> > 3.68   3.49 3.5 0.9 0.8  1.092  1.059  0.986  1.101
> 0.299  0.882  0.968
> > 3.49   3.34 2.6 0.9 0.8  1.092  1.382  1.298  1.438
> 0.395  0.829  0.952
> > 3.34   3.21 2.1 0.9 0.8  1.084  1.543  1.489  1.614
> 0.468  0.772  0.933
> > 3.21   3.10 1.6 0.9 0.8  1.070  1.591  1.669  1.680
> 0.529  0.645  0.885
> >All reflections  5.0 0.8 0.6  1.048  0.538  0.487  0.559
> 0.153
> >
> > Thank you.
> >
> > Liang
> >
> >
> >
> --
> >
> > To unsubscribe from the CCP4BB list, click the following link:
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> >
>
> 
>
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Re: [ccp4bb] R-merge is too high !!

[Edward A. Berry]

The fact that chi^2 is approximately 1.0 in all shells says that the deviations 
are about what is expected from the error model. The fact that Rpim is much 
lower than Rmeas means that you have rather high redundancy. This would seem to 
be a case of collecting low dose per image and making up for it with high 
redundancy, a strategy that has been recommended to ensure a full dataset even 
in the case of high radiation sensitivity.  In my opinion the high Rmerge is 
nothing to worry about. Look instead at CC1/2 and I/sigI which seem fine.

On 09/28/2018 04:09 AM, Zhang Foggy wrote:

Dear All,

Sorry for the off-topic.

I recently collected a set of data. The diffraction spots are extremely sharp. 
However, When I used HKL3000 to scale it, I get a final resolution at 3.1A with 
overall R-merge ~0.54 (R-merge in the highest 3.2A-3.1A shell: 1.59). Then I 
solve the structure with final R value 0.19 and R free value 0.24 although I 
know this Rmerge value is totally unacceptable, and the density looks perfect.

I also tried to collect other four set of data with different crystals. 
unfortunately, all of them have same problem.

I ask one of my friend who is an expert in HKL3000, but he had no idea about 
it. Does anyone has suggestions?

Here is the scale information for your review:
Space group: P43 (I also tried P1, the Rmerge value is still similar)

Shell Lower Upper Average  Average Norm. Linear Square
  limitAngstrom   I   error   stat. Chi**2  R-fac  R-fac  Rmeas   Rpim  
CC1/2CC*
   50.00   6.6711.6 0.9 0.3  1.165  0.191  0.284  0.198  0.052  
0.975  0.994
6.67   5.30 4.5 0.5 0.3  0.952  0.317  0.313  0.329  0.086  
0.971  0.993
5.30   4.63 7.3 0.7 0.5  0.961  0.293  0.297  0.304  0.081  
0.975  0.994
4.63   4.21 7.0 0.8 0.6  0.986  0.369  0.358  0.382  0.101  
0.969  0.992
4.21   3.91 5.6 0.8 0.6  1.040  0.522  0.491  0.541  0.142  
0.955  0.988
3.91   3.68 4.6 0.9 0.7  1.064  0.718  0.669  0.746  0.203  
0.929  0.981
3.68   3.49 3.5 0.9 0.8  1.092  1.059  0.986  1.101  0.299  
0.882  0.968
3.49   3.34 2.6 0.9 0.8  1.092  1.382  1.298  1.438  0.395  
0.829  0.952
3.34   3.21 2.1 0.9 0.8  1.084  1.543  1.489  1.614  0.468  
0.772  0.933
3.21   3.10 1.6 0.9 0.8  1.070  1.591  1.669  1.680  0.529  
0.645  0.885
   All reflections  5.0 0.8 0.6  1.048  0.538  0.487  0.559  0.153

Thank you.

Liang


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[ccp4bb] Two positions for Associate Research Scientists, Protein Crystallization at Bristol-Myers Squibb Princeton, NJ, USA

[Sheriff, Steven]

Bristol-Myers Squibb has two open positions for Associate Research Scientists, 
Protein Crystallization

The only way to apply for these positions are at the following URLs:

https://www.linkedin.com/jobs/view/868141001/
https://www.linkedin.com/jobs/view/868855975/

[If you have questions, please contact 
shannon.ke...@bms.com, Talent Acquisition 
Specialist, R&D]

Job description

Bristol-Myers Squibb is a global biopharmaceutical company whose mission is to 
discover, develop and deliver innovative medicines that help patients prevail 
over serious diseases.

One shared journey is moving us forward at Bristol-Myers Squibb. Around the 
world, we are passionate about making an impact on the lives of patients with 
serious disease. Empowered to apply our individual talents and ideas so that we 
can learn and grow together. Driven to make a difference, from innovative 
research to hands-on community support. Bristol-Myers Squibb recognizes the 
importance of balance and flexibility in our work environment. We offer a wide 
variety of competitive benefits, services and programs that provide our 
employees the resources to pursue their goals, both at work and in their 
personal lives.

Responsibilities Required

As a key member of the Molecular Structure & Design group, the successful 
candidate will be responsible for crystallization, purification and 
characterization of recombinant proteins utilizing knowledge of conventional 
and affinity chromatography methods, gel electrophoresis, crystallization, and 
general laboratory procedures. As a member of a team involved in the early 
stages of discovery, the position requires close collaboration with molecular 
biologists, protein scientists and structural biologists as well as scientists 
working in the various disease biology and translational areas within 
preclinical research. The candidate must be self motivated, possess excellent 
communication skills, and work both independently as well as in teams. Personal 
attributes of integrity and scientific creativity are required.

Major Skills Required
* BS/MS in Biochemistry, Structural Biology or related field plus 2-6 years of 
experience of industry or academia
* Carry out protein crystallization experiments, crystallization optimization, 
crystal harvesting for proteins and protein ligand complexes.
* Utilize crystallization automation equipment (liquid handlers, drop setters, 
imagers, etc.)
* Carry out protein purification / characterization as well as a thorough 
understanding of protein chromatography principles.
* Capable of independently designing experiments, generating data and 
interpreting results; demonstrated ability to work in a team environment.
* Possesses strong communication skills - be a good listener, have strong, 
concise, and consistent written and oral communication skills.
* The following skills, while not required, would be a plus
*Ability to independently troubleshoot purification systems and protocols.
*Experience in E. coli fermentation and protein expression.
*Experience in X-ray data collection and knowledge of X-ray structure analysis 
is a plus.

This message (including any attachments) may contain confidential, proprietary, 
privileged and/or private information. The information is intended to be for 
the use of the individual or entity designated above. If you are not the 
intended recipient of this message, please notify the sender immediately, and 
delete the message and any attachments. Any disclosure, reproduction, 
distribution or other use of this message or any attachments by an individual 
or entity other than the intended recipient is prohibited.



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[ccp4bb] Deadline for Diamond XChem proposals next Wednesday

[Frank von Delft]

Dear aspiring drug discoverers

A reminder that the deadline for the next round of proposals for XChem 
fragment screening is *next Wednesday*, as part of Diamond's general 
Call for Proposals.


Full details 
 
are on the XChem webpage 
.


*NEW*:  we are now inviting a broader set of projects:

 * Two-tiered access:  if you have an exciting system but don't yet
   know how to progress it, you can ask for exploratory access ("Tier 1")
 * BAG access:  several labs and collaborations have requested
   increased flexibility, and they can now apply as Block Allocation
   Groups.  If you wish to submit this route, I suggest you also email
   me directly.

Happy screening!

Frank


--
Prof Frank von Delft
Associate Professor Principal Investigator: Protein Crystallography
Structural Genomics Consortium
Oxford University
+44 1865 617583 (office: W,F)

Principal Beamline Scientist: I04-1
Diamond Light Source
+44 1235 778997 (office: M,T,T)
+44 7471 026103 (mobile)



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Re: [ccp4bb] R-merge is too high !!

[Ditlev Egeskov Brodersen]

1) Double check space group (run POINTLESS with unmerged data).
2) Process only as much data as needed for full completenes and see what you 
get (Rpim is OK, so the means of your structure factors are good, which also is 
consistent with your low refinement R factors and the maps).

Best,

Ditlev

---

Ditlev E. Brodersen
Lektor, Associate Professor
Department of Molecular Biology and Genetics, Aarhus University
Gustav Wieds Vej 10c, DK-8000 Aarhus C, Denmark

Phone:  +45 21669001
Lab home page: www.bioxray.au.dk/~deb
Educational IT portal: curriculearn.dk

On 28 Sep 2018, at 10.09, Zhang Foggy 
mailto:foggyc...@gmail.com>> wrote:

Dear All,

Sorry for the off-topic.

I recently collected a set of data. The diffraction spots are extremely sharp. 
However, When I used HKL3000 to scale it, I get a final resolution at 3.1A with 
overall R-merge ~0.54 (R-merge in the highest 3.2A-3.1A shell: 1.59). Then I 
solve the structure with final R value 0.19 and R free value 0.24 although I 
know this Rmerge value is totally unacceptable, and the density looks perfect.

I also tried to collect other four set of data with different crystals. 
unfortunately, all of them have same problem.

I ask one of my friend who is an expert in HKL3000, but he had no idea about 
it. Does anyone has suggestions?

Here is the scale information for your review:
Space group: P43 (I also tried P1, the Rmerge value is still similar)

Shell Lower Upper Average  Average Norm. Linear Square
 limitAngstrom   I   error   stat. Chi**2  R-fac  R-fac  Rmeas   Rpim  
CC1/2CC*
  50.00   6.6711.6 0.9 0.3  1.165  0.191  0.284  0.198  0.052  
0.975  0.994
   6.67   5.30 4.5 0.5 0.3  0.952  0.317  0.313  0.329  0.086  
0.971  0.993
   5.30   4.63 7.3 0.7 0.5  0.961  0.293  0.297  0.304  0.081  
0.975  0.994
   4.63   4.21 7.0 0.8 0.6  0.986  0.369  0.358  0.382  0.101  
0.969  0.992
   4.21   3.91 5.6 0.8 0.6  1.040  0.522  0.491  0.541  0.142  
0.955  0.988
   3.91   3.68 4.6 0.9 0.7  1.064  0.718  0.669  0.746  0.203  
0.929  0.981
   3.68   3.49 3.5 0.9 0.8  1.092  1.059  0.986  1.101  0.299  
0.882  0.968
   3.49   3.34 2.6 0.9 0.8  1.092  1.382  1.298  1.438  0.395  
0.829  0.952
   3.34   3.21 2.1 0.9 0.8  1.084  1.543  1.489  1.614  0.468  
0.772  0.933
   3.21   3.10 1.6 0.9 0.8  1.070  1.591  1.669  1.680  0.529  
0.645  0.885
  All reflections  5.0 0.8 0.6  1.048  0.538  0.487  0.559  0.153

Thank you.

Liang




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Re: [ccp4bb] R-merge is too high !!

[Phil Evans]

It is well known that Rmerge is a terrible criterion for determining a 
resolution cutoff, see eg
P.A.Karplus,K.Diederichs,Science336,1030(2012)

As the intensities get weaker at high resolution, Rmerge tends to infinity, 
with no sensible cutoff. CC(1/2) is generally considered the best criterion for 
this, at present anyway. Rmerge of 1.59 in the outer shell is perfectly 
acceptable, CC(1/2) in the outer shell is 0.645 which is still good (maybe the 
data go a little beyond there?)

On the other hand, a high Rmerge (or low CC(1/2)) at low resolution, or in the 
top intensity bin, is a indicator of something seriously wrong, some horrible 
systematic error or instability. In your innermost resolution bin, the Rmerge 
values are rather high (what are Norm R-fac and Linear R-fac?), and CC(1/2) is 
a little low

You need to look at other things, notably radiation damage

But if the structure tells you what you want know, enjoy it!

Phil

> On 28 Sep 2018, at 09:09, Zhang Foggy  wrote:
> 
> Dear All,
> 
> Sorry for the off-topic. 
> 
> I recently collected a set of data. The diffraction spots are extremely 
> sharp. However, When I used HKL3000 to scale it, I get a final resolution at 
> 3.1A with overall R-merge ~0.54 (R-merge in the highest 3.2A-3.1A shell: 
> 1.59). Then I solve the structure with final R value 0.19 and R free value 
> 0.24 although I know this Rmerge value is totally unacceptable, and the 
> density looks perfect.
> 
> I also tried to collect other four set of data with different crystals. 
> unfortunately, all of them have same problem. 
> 
> I ask one of my friend who is an expert in HKL3000, but he had no idea about 
> it. Does anyone has suggestions?
> 
> Here is the scale information for your review:
> Space group: P43 (I also tried P1, the Rmerge value is still similar)
> 
> Shell Lower Upper Average  Average Norm. Linear Square
>  limitAngstrom   I   error   stat. Chi**2  R-fac  R-fac  Rmeas   Rpim 
>  CC1/2CC*
>   50.00   6.6711.6 0.9 0.3  1.165  0.191  0.284  0.198  0.052 
>  0.975  0.994
>6.67   5.30 4.5 0.5 0.3  0.952  0.317  0.313  0.329  0.086 
>  0.971  0.993
>5.30   4.63 7.3 0.7 0.5  0.961  0.293  0.297  0.304  0.081 
>  0.975  0.994
>4.63   4.21 7.0 0.8 0.6  0.986  0.369  0.358  0.382  0.101 
>  0.969  0.992
>4.21   3.91 5.6 0.8 0.6  1.040  0.522  0.491  0.541  0.142 
>  0.955  0.988
>3.91   3.68 4.6 0.9 0.7  1.064  0.718  0.669  0.746  0.203 
>  0.929  0.981
>3.68   3.49 3.5 0.9 0.8  1.092  1.059  0.986  1.101  0.299 
>  0.882  0.968
>3.49   3.34 2.6 0.9 0.8  1.092  1.382  1.298  1.438  0.395 
>  0.829  0.952
>3.34   3.21 2.1 0.9 0.8  1.084  1.543  1.489  1.614  0.468 
>  0.772  0.933
>3.21   3.10 1.6 0.9 0.8  1.070  1.591  1.669  1.680  0.529 
>  0.645  0.885
>   All reflections  5.0 0.8 0.6  1.048  0.538  0.487  0.559  0.153
> 
> Thank you.  
> 
> Liang
> 
> 
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[ccp4bb] Job Offer: Group Leader in Structural biology or Biochemistry

[Fan Jiang]

Dear colleagues,   

Viva Biotech, located in Shanghai, China, is specialized in structure-based 
drug discovery providing preclinical drug discovery research services to global 
pharmaceutical and biotech companies. We have opening for program leader in 
structural biology and biochemistry. Anyone who is interested in the position  
please send CV to jin@vivabiotech.com.   

Job title: Group Leader in Structural Biology or Biochemistry

Job description

We are seeking a highly motivated individual with experience in protein 
biochemistry and structural biology. Candidates will lead the structural 
biology team to carry out the biochemistry studies and/or gene-to-structure 
studies which elucidate the interactions between small molecules/peptides and 
their targets. Experiences with protein expression and purification, excellent 
interpersonal and managerial skills, team player with excellent written and 
verbal communication skills and proficiency in structure biology related 
software. Excellent communication skill in English; 3-5 years working 
experiences with in US or Europe.

Qualifications

1)  Ph.D. in crystallography or protein biochemistry training with minimal 
3-5 years’ working experience 

2)  Hands-on experience in protein crystallization, and protein expression 
and purification is optional. 

3)  Proficient in structure biology related software is plus. 

4)  Demonstrated managerial skill to guide groups through corporate change 
and growth. 

5)  Excellent verbal and writing skills in English are essential.

6)  Strong communication skills and client interaction are required.



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[ccp4bb] AW: [EXTERNAL] [ccp4bb] R-merge is too high !!

[Herman . Schreuder]

Dear Liang,

The first thing I would do is to look through your complete scan. ADXV has an 
option to display a movie of all images. It might be that some regions of your 
scan are very weak or otherwise bad. Merging these regions with good regions 
will produce high Rmerges.
I would also check for overloads and/or ice rings. These may wreak havoc on 
your scaling which, again, may produce very high Rmerges.
I would also try some other processing program (xds, mosflm, dials….), maybe 
one of these does not suffer from the scaling problem.
You should also process maybe just the first 30 or 40 frames to see what kind 
of Rmerges come out then.

Good luck!
Herman

Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Zhang 
Foggy
Gesendet: Freitag, 28. September 2018 10:10
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [EXTERNAL] [ccp4bb] R-merge is too high !!

Dear All,

Sorry for the off-topic.

I recently collected a set of data. The diffraction spots are extremely sharp. 
However, When I used HKL3000 to scale it, I get a final resolution at 3.1A with 
overall R-merge ~0.54 (R-merge in the highest 3.2A-3.1A shell: 1.59). Then I 
solve the structure with final R value 0.19 and R free value 0.24 although I 
know this Rmerge value is totally unacceptable, and the density looks perfect.

I also tried to collect other four set of data with different crystals. 
unfortunately, all of them have same problem.

I ask one of my friend who is an expert in HKL3000, but he had no idea about 
it. Does anyone has suggestions?

Here is the scale information for your review:
Space group: P43 (I also tried P1, the Rmerge value is still similar)

Shell Lower Upper Average  Average Norm. Linear Square
 limitAngstrom   I   error   stat. Chi**2  R-fac  R-fac  Rmeas   Rpim  
CC1/2CC*
  50.00   6.6711.6 0.9 0.3  1.165  0.191  0.284  0.198  0.052  
0.975  0.994
   6.67   5.30 4.5 0.5 0.3  0.952  0.317  0.313  0.329  0.086  
0.971  0.993
   5.30   4.63 7.3 0.7 0.5  0.961  0.293  0.297  0.304  0.081  
0.975  0.994
   4.63   4.21 7.0 0.8 0.6  0.986  0.369  0.358  0.382  0.101  
0.969  0.992
   4.21   3.91 5.6 0.8 0.6  1.040  0.522  0.491  0.541  0.142  
0.955  0.988
   3.91   3.68 4.6 0.9 0.7  1.064  0.718  0.669  0.746  0.203  
0.929  0.981
   3.68   3.49 3.5 0.9 0.8  1.092  1.059  0.986  1.101  0.299  
0.882  0.968
   3.49   3.34 2.6 0.9 0.8  1.092  1.382  1.298  1.438  0.395  
0.829  0.952
   3.34   3.21 2.1 0.9 0.8  1.084  1.543  1.489  1.614  0.468  
0.772  0.933
   3.21   3.10 1.6 0.9 0.8  1.070  1.591  1.669  1.680  0.529  
0.645  0.885
  All reflections  5.0 0.8 0.6  1.048  0.538  0.487  0.559  0.153

Thank you.

Liang




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[ccp4bb] R-merge is too high !!

[Zhang Foggy]

Dear All,

Sorry for the off-topic.

I recently collected a set of data. The diffraction spots are extremely
sharp. However, When I used HKL3000 to scale it, I get a final resolution
at 3.1A with overall R-merge ~0.54 (R-merge in the highest 3.2A-3.1A shell:
1.59). Then I solve the structure with final R value 0.19 and R free value
0.24 although I know this Rmerge value is totally unacceptable, and the
density looks perfect.

I also tried to collect other four set of data with different crystals.
unfortunately, all of them have same problem.

I ask one of my friend who is an expert in HKL3000, but he had no idea
about it. Does anyone has suggestions?

Here is the scale information for your review:
Space group: P43 (I also tried P1, the Rmerge value is still similar)

Shell Lower Upper Average  Average Norm. Linear Square
 limitAngstrom   I   error   stat. Chi**2  R-fac  R-fac  Rmeas
 Rpim  CC1/2CC*
  50.00   6.6711.6 0.9 0.3  1.165  0.191  0.284  0.198
0.052  0.975  0.994
   6.67   5.30 4.5 0.5 0.3  0.952  0.317  0.313  0.329
0.086  0.971  0.993
   5.30   4.63 7.3 0.7 0.5  0.961  0.293  0.297  0.304
0.081  0.975  0.994
   4.63   4.21 7.0 0.8 0.6  0.986  0.369  0.358  0.382
0.101  0.969  0.992
   4.21   3.91 5.6 0.8 0.6  1.040  0.522  0.491  0.541
0.142  0.955  0.988
   3.91   3.68 4.6 0.9 0.7  1.064  0.718  0.669  0.746
0.203  0.929  0.981
   3.68   3.49 3.5 0.9 0.8  1.092  1.059  0.986  1.101
0.299  0.882  0.968
   3.49   3.34 2.6 0.9 0.8  1.092  1.382  1.298  1.438
0.395  0.829  0.952
   3.34   3.21 2.1 0.9 0.8  1.084  1.543  1.489  1.614
0.468  0.772  0.933
   3.21   3.10 1.6 0.9 0.8  1.070  1.591  1.669  1.680
0.529  0.645  0.885
  All reflections  5.0 0.8 0.6  1.048  0.538  0.487  0.559
0.153

Thank you.

Liang



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