[ccp4bb] Postdoctoral position at the University of Oklahoma

[Thomas, Leonard M.]

I am posting this a faculty member here.  Please address any questions to her.

Postdoctoral position available immediately in Singh Group at OU.
Biochemist or Structural Biologist: Seeking a highly motivated postdoc with 
experience in one or more biochemical techniques involving cloning, protein 
expression, engineering (site-directed, site-saturation and random mutation) 
purification, biochemical assays, X-ray crystallography, structure 
calculations, and functional characterization of enzymes. The ideal applicant 
should have a Ph.D. in Biochemistry or related area. The candidate should have 
expertise in determining X-ray structures of enzymes, functional 
characterization, and engineering studies for their potential as biocatalysts 
for drug development. If you are interested in applying, please email your CV 
to shanteri.si...@ou.edu
Research Overview in Singh Group
Research in the Singh laboratory lies at the interface of chemistry and 
biochemistry. We use tools and methods from biochemistry and structural biology 
to characterize new enzymes from natural product biosynthetic pathways; 
molecular biology techniques to engineer enzymes to generate better 
biocatalysts; and synthetic chemistry methods for the generation of precursors 
necessary for natural product diversification. The fundamental goal of research 
in Singh laboratory is to understand and exploit natural product enzymes for 
developing biologically active molecules against cancer and infectious 
diseases. Our lab is especially interested in exploiting the ability of late 
stage enzymes from natural product biosynthetic pathways for the structural 
diversification of complex natural products. Despite the fact that structural 
diversification of biologically active molecules by attaching different 
chemical moieties has great potential to generate new drug leads, chemical 
methods often suffer from selectivity and tedious purification steps. Our goal 
is to exploit the potential of natural product enzymes and generate 
chemoenzymatic-tools for facile attachment of chemical moieties in a stereo- 
and regio- selective fashion to complex molecules towards the generation of 
biologically active compounds.



Leonard Thomas
lmtho...@ou.edu






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Re: [ccp4bb] refinement of 0.73A data in shelxl

[00000c2488af9525-dmarc-request]

Remembered earlier that if the "CL" is not shifted one place to the left, Shelx and probably most other programs treat it as carbon, i.e. its assumed to have 6 rather than 17 electrons. Trust occupancies OK, too ;-?Jon CooperOn 3 Feb 2020 18:26, "Barone, Matthias"  wrote:


Hi Pavel
glad you write me. I was hoping you would read my post.
- Yes, protons are added, both on the protein as well as on the molecule
- I initially only refined protein and ligand anisotropically, now Im running a refinement with all atoms anisotrp except Hs. This would then also be the same as shelxl is doing.
- Alternate conformations are modeled, also on the ligand. There are plenty, sure, but I think I got most of them.
- I already used Water update during refine, there are some NO3s in the structure. I got them in. There is a second ligand somewhere as artifact. its density is not well defined, so I hope to get that in once the map clears up more. 
- I let phenix.refine optimize adp and chemisty weights, but as Petri suggested, Im manually increasing the scale factors to match the ones from shelxl (just to compare them properly). Im aiming for an rsmd of 0.02-0.03A like Petri suggested and keep an
 eye on how tight the structure is refined in shelxl.


About the Rfact and the gap. Yes, thats what I was expecting. I hope if I add more anisotropic B fact, the Rfacts should go down to at least what shelxl yielded. 


thank you all again for the massive feedback, ideas and help. 








Dr. Matthias Barone
AG Kuehne, Rational Drug Design

Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)
Robert-Rössle-Strasse 10
13125 Berlin
Germany
Phone: +49 (0)30 94793-284





From: Pavel Afonine 
Sent: Monday, February 3, 2020 7:14:25 PM
To: Barone, Matthias
Cc: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] refinement of 0.73A data in shelxl
 



Hi Matthias,


did you use correct model parameterization and optimal refinement strategy for the resolution? Such as:
- Add H atoms;
- Refine all but H atoms with anisotropic ADPs;
- Model alternative conformations (that one'd expect many at this resolution);
- Add solvent (water, crystallization cocktail components if you see any);
- Relax restraints on geometry and ADPs;
 long list!


If not, then what you have in terms of R factors is more or less what I'd expect.


In the absence of obvious data pathologies, I'd expect Rwork/Rfree in 10-15% range, and the Rfree-Rwork gap around 1-2% or less.


Since you mentioned Phenix refinement, I am happy to help you with details etc off-list.


Pavel


On Mon, Feb 3, 2020 at 3:08 AM Barone, Matthias  wrote:




Dear ccp4 community
Im having some problems solving a 0.73A structure. Spacegroup seems to be correct,
 data are not twinned, 95.5% overall completeness, ISa 25.6. Outer shell CC1/2
 24% and 90.4% complete.
The model is nearly fully built, there is no remaining unmodelled areas. However, Rfact
is stuck 27% in phenix, with a very distinct artifact in the electron map (see phenix.jpg). You can see difference
 density on various well defined sidechain atoms. Notably, they seem to follow a pattern: Nearly all Val CG have difference signal, as well as many backbone NH. Hence, I suspected that it might be a problem with the SF, since
 we recorded the DS at 0.86A. 



Hence I gave shelxl a shot:
I used the refined model from phenix, converted it via pdb2ins and pasted the restraints created by prodrg. 
The shelxl hkl was produced by xdsconv, using the freeR flagging of the mtz used by phenix (no merge, friedel false).
Interestingly, shelxl can bring Rfree down to 16% and almost all of the diff-density artifacts seen before are gone (shelxl_noSFAC-CL.jpg). Except one: the inhibitor contains a chlorinated phenylring (pdb
 ligand 2L5) which now shows massive difference density for Cl. 
I therefore suggested that I might deal with a wrong SF for Cl. Funny enough, pdb2ins does not produce a DISP line for Cl if converting the pdb that contains the inhibitor. Hence,
I used pdb2ins and the pdb from PRODRG to produce SFAC for the inhibitor Cloride. I then pasted this line

DISP $CL    0.18845    0.21747   1035.16450

into the .res file and updated the UNIT line. Shelxl runs through, and the density looks ok on the Chloride now. However Rfree is back
 up at 24% and the artifacts seen by phenix.refine are back (shelxl_SFAC-CL.jpg): now, very distincitvly, backbone carbonyls and NHs show difference
 density.

Am I right in my assumption, that the SFAC of Cloride is not properly calculated at the given wavelenght? And if so, how do I guess it correctly?


Thank you very much for your help!
Best, matthias








Dr. Matthias Barone
AG Kuehne, Rational Drug Design

Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)
Robert-Rössle-Strasse 10
13125 Berlin
Germany
Phone: +49 (0)30 94793-284







To u

Re: [ccp4bb] refinement of 0.73A data in shelxl

[Barone, Matthias]

Hi Pavel

glad you write me. I was hoping you would read my post.

- Yes, protons are added, both on the protein as well as on the molecule

- I initially only refined protein and ligand anisotropically, now Im running a 
refinement with all atoms anisotrp except Hs. This would then also be the same 
as shelxl is doing.

- Alternate conformations are modeled, also on the ligand. There are plenty, 
sure, but I think I got most of them.

- I already used Water update during refine, there are some NO3s in the 
structure. I got them in. There is a second ligand somewhere as artifact. its 
density is not well defined, so I hope to get that in once the map clears up 
more.

- I let phenix.refine optimize adp and chemisty weights, but as Petri 
suggested, Im manually increasing the scale factors to match the ones from 
shelxl (just to compare them properly). Im aiming for an rsmd of 0.02-0.03A 
like Petri suggested and keep an eye on how tight the structure is refined in 
shelxl.


About the Rfact and the gap. Yes, thats what I was expecting. I hope if I add 
more anisotropic B fact, the Rfacts should go down to at least what shelxl 
yielded.


thank you all again for the massive feedback, ideas and help.




Dr. Matthias Barone

AG Kuehne, Rational Drug Design

Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)
Robert-Rössle-Strasse 10
13125 Berlin

Germany
Phone: +49 (0)30 94793-284


From: Pavel Afonine 
Sent: Monday, February 3, 2020 7:14:25 PM
To: Barone, Matthias
Cc: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] refinement of 0.73A data in shelxl

Hi Matthias,

did you use correct model parameterization and optimal refinement strategy for 
the resolution? Such as:
- Add H atoms;
- Refine all but H atoms with anisotropic ADPs;
- Model alternative conformations (that one'd expect many at this resolution);
- Add solvent (water, crystallization cocktail components if you see any);
- Relax restraints on geometry and ADPs;
 long list!

If not, then what you have in terms of R factors is more or less what I'd 
expect.

In the absence of obvious data pathologies, I'd expect Rwork/Rfree in 10-15% 
range, and the Rfree-Rwork gap around 1-2% or less.

Since you mentioned Phenix refinement, I am happy to help you with details etc 
off-list.

Pavel

On Mon, Feb 3, 2020 at 3:08 AM Barone, Matthias 
mailto:bar...@fmp-berlin.de>> wrote:

Dear ccp4 community

Im having some problems solving a 0.73A structure. Spacegroup seems to be 
correct, data are not twinned, 95.5% overall completeness, ISa 25.6. Outer 
shell CC1/2 24% and 90.4% complete.

The model is nearly fully built, there is no remaining unmodelled areas. 
However, Rfact is stuck 27% in phenix, with a very distinct artifact in the 
electron map (see phenix.jpg). You can see difference density on various well 
defined sidechain atoms. Notably, they seem to follow a pattern: Nearly all Val 
CG have difference signal, as well as many backbone NH. Hence, I suspected that 
it might be a problem with the SF, since we recorded the DS at 0.86A.


Hence I gave shelxl a shot:

I used the refined model from phenix, converted it via pdb2ins and pasted the 
restraints created by prodrg.

The shelxl hkl was produced by xdsconv, using the freeR flagging of the mtz 
used by phenix (no merge, friedel false).

Interestingly, shelxl can bring Rfree down to 16% and almost all of the 
diff-density artifacts seen before are gone (shelxl_noSFAC-CL.jpg). Except one: 
the inhibitor contains a chlorinated phenylring (pdb ligand 2L5) which now 
shows massive difference density for Cl.

I therefore suggested that I might deal with a wrong SF for Cl. Funny enough, 
pdb2ins does not produce a DISP line for Cl if converting the pdb that contains 
the inhibitor. Hence, I used pdb2ins and the pdb from PRODRG to produce SFAC 
for the inhibitor Cloride. I then pasted this line

DISP $CL0.188450.21747   1035.16450

into the .res file and updated the UNIT line. Shelxl runs through, and the 
density looks ok on the Chloride now. However Rfree is back up at 24% and the 
artifacts seen by phenix.refine are back (shelxl_SFAC-CL.jpg): now, very 
distincitvly, backbone carbonyls and NHs show difference density.

Am I right in my assumption, that the SFAC of Cloride is not properly 
calculated at the given wavelenght? And if so, how do I guess it correctly?


Thank you very much for your help!

Best, matthias




Dr. Matthias Barone

AG Kuehne, Rational Drug Design

Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)
Robert-Rössle-Strasse 10
13125 Berlin

Germany
Phone: +49 (0)30 94793-284



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Re: [ccp4bb] refinement of 0.73A data in shelxl

[Pavel Afonine]

Hi Matthias,

did you use correct model parameterization and optimal refinement strategy
for the resolution? Such as:
- Add H atoms;
- Refine all but H atoms with anisotropic ADPs;
- Model alternative conformations (that one'd expect many at this
resolution);
- Add solvent (water, crystallization cocktail components if you see any);
- Relax restraints on geometry and ADPs;
 long list!

If not, then what you have in terms of R factors is more or less what I'd
expect.

In the absence of obvious data pathologies, I'd expect Rwork/Rfree in
10-15% range, and the Rfree-Rwork gap around 1-2% or less.

Since you mentioned Phenix refinement, I am happy to help you with details
etc off-list.

Pavel

On Mon, Feb 3, 2020 at 3:08 AM Barone, Matthias 
wrote:

> Dear ccp4 community
>
> Im having some problems solving a 0.73A structure. Spacegroup seems to be
> correct, data are not twinned, 95.5% overall completeness, ISa 25.6. Outer
> shell CC1/2 24% and 90.4% complete.
>
> The model is nearly fully built, there is no remaining unmodelled areas.
> However, Rfact is stuck 27% in phenix, with a very distinct artifact in
> the electron map (see phenix.jpg). You can see difference density on
> various well defined sidechain atoms. Notably, they seem to follow a
> pattern: Nearly all Val CG have difference signal, as well as many backbone
> NH. Hence, I suspected that it might be a problem with the SF, since we
> recorded the DS at 0.86A.
>
>
> Hence I gave shelxl a shot:
>
> I used the refined model from phenix, converted it via pdb2ins and pasted
> the restraints created by prodrg.
>
> The shelxl hkl was produced by xdsconv, using the freeR flagging of the
> mtz used by phenix (no merge, friedel false).
>
> Interestingly, shelxl can bring Rfree down to 16% and almost all of
> the diff-density artifacts seen before are gone (shelxl_noSFAC-CL.jpg).
> Except one: the inhibitor contains a chlorinated phenylring (pdb ligand
> 2L5) which now shows massive difference density for Cl.
>
> I therefore suggested that I might deal with a wrong SF for Cl. Funny
> enough, pdb2ins does not produce a DISP line for Cl if converting the pdb
> that contains the inhibitor. Hence, I used pdb2ins and the pdb from
> PRODRG to produce SFAC for the inhibitor Cloride. I then pasted this line
>
> DISP $CL0.188450.21747   1035.16450
>
> into the .res file and updated the UNIT line. Shelxl runs through, and
> the density looks ok on the Chloride now. However Rfree is back up at 24%
> and the artifacts seen by phenix.refine are back (shelxl_SFAC-CL.jpg):
> now, very distincitvly, backbone carbonyls and NHs show difference density.
>
> Am I right in my assumption, that the SFAC of Cloride is not properly
> calculated at the given wavelenght? And if so, how do I guess it correctly?
>
>
> Thank you very much for your help!
>
> Best, matthias
>
>
>
>
> Dr. Matthias Barone
>
> AG Kuehne, Rational Drug Design
>
> Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)
> Robert-Rössle-Strasse 10
> 13125 Berlin
>
> Germany
> Phone: +49 (0)30 94793-284
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
>



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[ccp4bb] PhD opportunities in host-pathogen interactions and cryo-EM method development

[Arjen Jakobi - TNW]

Dear all,

we have two 4-year PhD opportunities in our lab at the Department of 
Bionanoscience, Kavli Institute of Nanoscience at Delft University of 
Technology.

Opportunities exist both for candidates with an interest in structural, 
functional and biophysical studies of host-pathogen interactions, and for 
candidates with an interest in cryo-EM method development.

Candidates for the PhD positions must have a MSc degree in molecular life 
science, (bio)chemistry, (bio)physics or (molecular and cellular) biology.

More details and requirements through the links below:


  *   PhD student in structural biology of host-pathogen 
interactions
 (TNWBN20-006)
  *   PhD student in cryo-EM method 
development
 (TNWBN20-007)

The Kavli Institute of Nanoscience at TU Delft is an exciting place to work at 
the interface of biology and physics and provides an international, dynamic and 
collaborative environment with state-of-the-art facilities (e.g. cryo-EM, MS, 
single-molecule biophysics, advanced light microscopy, protein and membrane 
biochemistry).

Delft is a friendly historic university city with a highly international 
population and a rich cultural scene, located at a short 30 min train ride from 
Schiphol International Airport with connections to almost any part in the world.

Come and join us.

Best,
Arjen


Arjen Jakobi
Kavli Institute of Nanoscience
TU Delft / Department of Bionanoscience
Van der Maasweg 9
2629 HZ Delft
T +31 (0) 15 278 9249
F +31 (0) 15 278 1202
E a.jak...@tudelft.nl
I  http://cryoem.tudelft.nl




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Re: [ccp4bb] Protein fold and the moonlighting function

[Emmanuel Saridakis]

I believe this is more than a fluke. It looks to me like a very powerful 
evolutionary tool which may have rendered the early stages in the evolution of 
life less improbable.
Best wishes,
Emmanuel Saridakis


- Original Message -
From: "Peter Stogios" 
To: "CCP4BB" 
Sent: Monday, 3 February, 2020 02:18:45
Subject: Re: [ccp4bb] Protein fold and the moonlighting function

I think you’re asking if two proteins with the same fold can have different 
activities.

As was previously mentioned, this is quite common.  The best characterized 
example is the TIM barrel fold - such proteins can be isomerases, transferases, 
hydrolases, lyases, or oxidoreductases, to name a few...



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Re: [ccp4bb] refinement of 0.73A data in shelxl

[00000c2488af9525-dmarc-request]

Hello, sorry if this is a really obvious question, but have you used the ANIS option? I remember it is good at cleaning-up difference density around halogen atoms that sort of resolution.Jon CooperOn 3 Feb 2020 11:08, "Barone, Matthias"  wrote:

Dear ccp4 community
Im having some problems solving a 0.73A structure. Spacegroup
 seems to be correct, data are not twinned, 95.5% overall completeness, ISa 25.6. Outer shell CC1/2
 24% and 90.4% complete.
The model is nearly fully built, there is no remaining unmodelled
 areas. However, Rfact is stuck 27% in phenix, with a very distinct artifact in the electron map (see phenix.jpg).
 You can see difference density on various well defined sidechain atoms. Notably, they seem to follow a pattern: Nearly all Val CG have difference signal, as well as many backbone NH. Hence, I suspected that it might be
 a problem with the SF, since we recorded the DS at 0.86A. 



Hence I gave shelxl a shot:
I used the refined model from phenix, converted it via pdb2ins and pasted the restraints created by prodrg. 
The shelxl hkl was produced by xdsconv, using the freeR flagging of the mtz used by phenix (no merge, friedel false).
Interestingly, shelxl can bring Rfree down to 16% and almost all of the diff-density artifacts seen before are gone (shelxl_noSFAC-CL.jpg). Except one: the inhibitor contains a chlorinated phenylring
 (pdb ligand 2L5) which now shows massive difference density for Cl. 
I therefore suggested that I might deal with a wrong SF for Cl. Funny enough, pdb2ins does not produce a DISP line for Cl if converting the pdb that contains the inhibitor. Hence,
I used pdb2ins and the pdb from PRODRG to produce SFAC for the inhibitor Cloride. I then pasted this line

DISP $CL    0.18845    0.21747   1035.16450

into the .res file and updated the UNIT line. Shelxl runs through, and the density looks ok on the Chloride now. However Rfree
 is back up at 24% and the artifacts seen by phenix.refine are back (shelxl_SFAC-CL.jpg): now, very distincitvly, backbone carbonyls and
 NHs show difference density.

Am I right in my assumption, that the SFAC of Cloride is not properly calculated at the given wavelenght? And if so, how do I guess it correctly?


Thank you very much for your help!
Best, matthias








Dr. Matthias Barone
AG Kuehne, Rational Drug Design

Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)
Robert-Rössle-Strasse 10
13125 Berlin
Germany
Phone: +49 (0)30 94793-284







To unsubscribe from the CCP4BB list, click the following link:
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Re: [ccp4bb] refinement of 0.73A data in shelxl

[Bernhard Rupp]

Maybe the figures were just contoured odd...but my recollection of a good
0.8 A map appearance is differentwhich might be consistent with the
high Rf...a look at the high res data or images/stats might help?

Best, br

On Mon, Feb 3, 2020, 14:58 George Sheldrick 
wrote:

> Dear Matthias,
>
>
> That is very strange. First please repeat the shelxl refinement with the
> occupancy of the offending chlorine(s) in the .ins file changed from 11
> (i.e. fixed at 1.0) to 1.0 (i.e. freely refined starting from 1.0). If that
> does not help I would be happy to look at it in confidence, I would need
> the .hkl and .ins files.
>
>
> Best wishes, George
>
>
>
>
> On 03.02.20 12:08, Barone, Matthias wrote:
>
> Dear ccp4 community
>
> Im having some problems solving a 0.73A structure. Spacegroup seems to be
> correct, data are not twinned, 95.5% overall completeness, ISa 25.6. Outer
> shell CC1/2 24% and 90.4% complete.
>
> The model is nearly fully built, there is no remaining unmodelled areas.
> However, Rfact is stuck 27% in phenix, with a very distinct artifact in
> the electron map (see phenix.jpg). You can see difference density on
> various well defined sidechain atoms. Notably, they seem to follow a
> pattern: Nearly all Val CG have difference signal, as well as many backbone
> NH. Hence, I suspected that it might be a problem with the SF, since we
> recorded the DS at 0.86A.
>
>
> Hence I gave shelxl a shot:
>
> I used the refined model from phenix, converted it via pdb2ins and pasted
> the restraints created by prodrg.
>
> The shelxl hkl was produced by xdsconv, using the freeR flagging of the
> mtz used by phenix (no merge, friedel false).
>
> Interestingly, shelxl can bring Rfree down to 16% and almost all of
> the diff-density artifacts seen before are gone (shelxl_noSFAC-CL.jpg).
> Except one: the inhibitor contains a chlorinated phenylring (pdb ligand
> 2L5) which now shows massive difference density for Cl.
>
> I therefore suggested that I might deal with a wrong SF for Cl. Funny
> enough, pdb2ins does not produce a DISP line for Cl if converting the pdb
> that contains the inhibitor. Hence, I used pdb2ins and the pdb from
> PRODRG to produce SFAC for the inhibitor Cloride. I then pasted this line
>
> DISP $CL0.188450.21747   1035.16450
>
> into the .res file and updated the UNIT line. Shelxl runs through, and
> the density looks ok on the Chloride now. However Rfree is back up at 24%
> and the artifacts seen by phenix.refine are back (shelxl_SFAC-CL.jpg):
> now, very distincitvly, backbone carbonyls and NHs show difference density.
>
> Am I right in my assumption, that the SFAC of Cloride is not properly
> calculated at the given wavelenght? And if so, how do I guess it correctly?
>
> Thank you very much for your help!
>
> Best, matthias
>
>
> Dr. Matthias Barone
>
> AG Kuehne, Rational Drug Design
>
> Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)
> Robert-Rössle-Strasse 10
> 13125 Berlin
>
> Germany
> Phone: +49 (0)30 94793-284
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
>
> --
> Prof. George M. Sheldrick FRS
> Dept. Structural Chemistry
> University of Goettingen
> Tammannstr.  4
> D37077 Goettingen
> Germany
> Tel: +49 551 3933021 or +49 5594 227312
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
>



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Re: [ccp4bb] refinement of 0.73A data in shelxl

[George Sheldrick]

Dear Matthias,


That is very strange. First please repeat the shelxl refinement with the 
occupancy of the offending chlorine(s) in the .ins file changed from 11  
(i.e. fixed at 1.0) to 1.0 (i.e. freely refined starting from 1.0). If 
that does not help I would be happy to look at it in confidence, I would 
need the .hkl and .ins files.



Best wishes, George




On 03.02.20 12:08, Barone, Matthias wrote:


Dear ccp4 community

Im having some problems solving a 0.73A structure. Spacegroup seems to 
be correct, data are not twinned, 95.5% overall completeness, ISa 
25.6. Outer shell CC1/2 24% and 90.4% complete.


The model is nearly fully built, there is no remaining unmodelled 
areas. However, Rfact isstuck 27% in phenix, with a very distinct 
artifact in the electron map (see phenix.jpg). You can see difference 
density on various well defined sidechain atoms. Notably, they seem to 
follow a pattern: Nearly all Val CG have difference signal, as well as 
many backbone NH. Hence, I suspected that it might be a problem with 
the SF, since we recorded the DS at 0.86A.



Hence I gave shelxl a shot:

I used the refined model from phenix, converted it via pdb2ins and 
pasted the restraints created by prodrg.


The shelxl hkl was produced by xdsconv, using the freeR flagging of 
the mtz used by phenix (no merge, friedel false).


Interestingly, shelxl can bring Rfree down to 16% and almost all of 
the diff-density artifacts seen before are 
gone (shelxl_noSFAC-CL.jpg). Except one: the inhibitor contains a 
chlorinated phenylring (pdb ligand 2L5) which now shows massive 
difference density for Cl.


I therefore suggested that I might deal with a wrong SF for Cl. Funny 
enough, pdb2ins does not produce a DISP line for Cl if converting the 
pdb that contains the inhibitor. Hence, I used pdb2ins and the pdb 
from PRODRG to produce SFAC for the inhibitor Cloride. I then pasted 
this line


DISP $CL    0.18845    0.21747   1035.16450

into the .res file andupdated the UNIT line. Shelxl runs through, and 
the density looks ok on the Chloride now. However Rfree is back up at 
24% and the artifacts seen by phenix.refine are back 
(shelxl_SFAC-CL.jpg): now, very distincitvly, backbone carbonyls and 
NHs show difference density.


Am I right in my assumption, that the SFAC of Cloride is not properly 
calculated at the given wavelenght? And if so, how do I guess it 
correctly?


Thank you very much for your help!

Best, matthias


Dr. Matthias Barone

AG Kuehne, Rational Drug Design

Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)
Robert-Rössle-Strasse 10
13125 Berlin

Germany
Phone: +49 (0)30 94793-284




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--
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry
University of Goettingen
Tammannstr.  4
D37077 Goettingen
Germany
Tel: +49 551 3933021 or +49 5594 227312




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[ccp4bb] Postdoc position available in Single Particle CryoEM or Cryo-ET, Southern University of Science and Technology, China

[Huawei Zhang]

Dear colleagues,

We are looking for motivated postdoc researchers to work in the field of
osteoarthritis and exosome biogenesis using Single Particle CryoEM or
Cryo-ET in Dr. Daping Wang and Dr. Huawei ZHANG’s lab. By a combination of
structural biology, cell biology, biochemistry and biophysics, we aim to
understand the molecular mechanism of osteoarthritis pathogenesis and
exosome biogenesis, and pave the way for drug design (small molecules and
antibodies etc). For more details about our research field, pls see
http://www.szklte.com/?m=home&c=View&a=index&aid=73 or
https://www.sustech.edu.cn/en/zhanghuawei.html?lang=en

Our lab is affiliated to Southern University of Science and Technology
(SUSTech), Shenzhen, China. SUStech is a rapidly developing university and
has set up China’s largest CryoEM centre with 6 300Kv Titan krios electron
microscopes, together with 71 sets of related auxiliary instruments and
sample preparation facilities. Plenty of time slots  will be available for
internal users.

The candidate should already or will obtain PhD degree in related fields
including structural biology, biochemistry, biophysics or molecular biology
etc. He or she should have at least 1 publication to demonstrate the track
record. Experience in cryo-electron microscopy or sample preparation is a
plus.

Competitive salary will be provided together with fringe benefit, housing
allowance and yearly bonus.

The position will be open until filled. Interested applicants please send
your CV (including basic info, education info, techniques and working
experiences etc) and contacts of two referees to Dr. Huawei ZHANG at
zhw2...@gmail.com.

Thank you for your attention.



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[ccp4bb] Postdoc Research Associate positions at Imperial College London

[Wilkinson, Martin]

Two Post-doctoral Research Associates Imperial College London

Reference: MED01520
Closing date: 27 February 2020

We are recruiting two Research Associates in the Section of Structural Biology 
at South Kensington in the research group of Professor Dale Wigley:

(https://www.imperial.ac.uk/people/d.wigley).

Duties and responsibilities

You will join a multi-disciplinary team of international researchers 
investigating the structures and mechanisms of chromatin modifying complexes in 
human DNA damage repair and cancer. We combine structural biology techniques 
(mainly cryoEM) with molecular biology/biochemistry to understand molecular 
mechanisms for DNA repair that prevent cancer in humans. Successful applicants 
will have proven expertise in either or both of these areas.

Essential requirements

You must hold a PhD, or equivalent, in biochemistry, enzymology or structural 
biology and have a demonstrated track record in conducting high quality 
original research. Experience at postgraduate or post-doctoral level in 
structural biology (crystallography or electron microscopy) and/or biochemistry 
is essential. Experience in expression/purification of multi-protein complexes 
in insect or human cells is desirable.

Further information

For informal enquiries please contact Professor Dale Wigley 
d.wig...@imperial.ac.uk. Visit 
www.imperial.ac.uk/jobs/description/MED01520/research-associate
 to apply. For technical issues when applying online please email 
recruitm...@imperial.ac.uk

Candidates who have not yet been officially awarded their PhD will be appointed 
as Research Assistant within the salary range £35,477- £38,566 per annum.

———
Dr Martin Wilkinson
mwilk...@ic.ac.uk

Imperial College
Lab 245
2nd Floor, SAF building
Imperial College Road
London
SW7 2AZ
———




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Re: [ccp4bb] refinement of 0.73A data in shelxl

[Eleanor Dodson]

The maps look beautiful, but maybe the high resolution data is refining
poorly.
Not sure how to do this with phenix or SHELX but REFMAC gives you a plot of
 and  v resolution. You sometimes see wild divergence in some
resolution shells.
Looking at Rfactors v resolution can also highlight such problems.

Eleanor


On Mon, 3 Feb 2020 at 11:08, Barone, Matthias  wrote:

> Dear ccp4 community
>
> Im having some problems solving a 0.73A structure. Spacegroup seems to be
> correct, data are not twinned, 95.5% overall completeness, ISa 25.6. Outer
> shell CC1/2 24% and 90.4% complete.
>
> The model is nearly fully built, there is no remaining unmodelled areas.
> However, Rfact is stuck 27% in phenix, with a very distinct artifact in
> the electron map (see phenix.jpg). You can see difference density on
> various well defined sidechain atoms. Notably, they seem to follow a
> pattern: Nearly all Val CG have difference signal, as well as many backbone
> NH. Hence, I suspected that it might be a problem with the SF, since we
> recorded the DS at 0.86A.
>
>
> Hence I gave shelxl a shot:
>
> I used the refined model from phenix, converted it via pdb2ins and pasted
> the restraints created by prodrg.
>
> The shelxl hkl was produced by xdsconv, using the freeR flagging of the
> mtz used by phenix (no merge, friedel false).
>
> Interestingly, shelxl can bring Rfree down to 16% and almost all of
> the diff-density artifacts seen before are gone (shelxl_noSFAC-CL.jpg).
> Except one: the inhibitor contains a chlorinated phenylring (pdb ligand
> 2L5) which now shows massive difference density for Cl.
>
> I therefore suggested that I might deal with a wrong SF for Cl. Funny
> enough, pdb2ins does not produce a DISP line for Cl if converting the pdb
> that contains the inhibitor. Hence, I used pdb2ins and the pdb from
> PRODRG to produce SFAC for the inhibitor Cloride. I then pasted this line
>
> DISP $CL0.188450.21747   1035.16450
>
> into the .res file and updated the UNIT line. Shelxl runs through, and
> the density looks ok on the Chloride now. However Rfree is back up at 24%
> and the artifacts seen by phenix.refine are back (shelxl_SFAC-CL.jpg):
> now, very distincitvly, backbone carbonyls and NHs show difference density.
>
> Am I right in my assumption, that the SFAC of Cloride is not properly
> calculated at the given wavelenght? And if so, how do I guess it correctly?
>
>
> Thank you very much for your help!
>
> Best, matthias
>
>
>
>
> Dr. Matthias Barone
>
> AG Kuehne, Rational Drug Design
>
> Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)
> Robert-Rössle-Strasse 10
> 13125 Berlin
>
> Germany
> Phone: +49 (0)30 94793-284
>
> --
>
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> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
>



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[ccp4bb] postdoc position in the Svergun group, EMBL Hamburg, P12 beamline

[Clement Blanchet]

Postdoctoral Fellow - Methods development for biological anomalous scattering

https://www.embl-hamburg.de/jobs/searchjobs/index.php?ref=HH00182&newlang=1&loc[]=3
 
https://www.embl-hamburg.de/jobs/searchjobs/index.php?ref=HH00182&newlang=1&loc[]=3


The European Molecular Biology Laboratory (EMBL) is one of the highest ranked 
scientific research organisations in the world. The Headquarters Laboratory is 
located in Heidelberg (Germany), with additional sites in Grenoble (France), 
Hamburg (Germany), Hinxton (UK), Monterotondo (Italy) and Barcelona (Spain).

The EMBL Hamburg Outstation at the DESY campus performs research in structural 
biology with specific emphasis on the use of synchrotron radiation. EMBL 
Hamburg runs two macromolecular crystallography (MX) beamlines and a Small 
Angle X-ray scattering (SAXS) beamline at the high-brillance storage ring PETRA 
III.

Applications are invited for a post-doctoral position in the BioSAXS group. The 
group has a strong experience in SAXS data collection and interpretation and 
runs the user-oriented P12 BioSAXS beamline at PETRA III.


Your role

You will work on the German Research Foundation (Deutsche 
Forschungsgemeinschaft, DFG) funded project on advanced approaches to study 
macromolecular structures in solution with anomalous SAXS (ASAXS). You will be 
involved in the experimental and computational methods development in 
collaboration with the University of Mainz, a partner on this DFG project.


You have

* A PhD in a relevant field (physics, mathematics, structural biology)
* Knowledge and/or interest in X-ray instrumentation
* Good communication and English language skills and the ability to collaborate 
with international teams are essential.


You might also have

Experience in programming and in biological scattering/diffraction would be 
advantageous.


Why join us

EMBL is an inclusive, equal opportunity employer offering attractive conditions 
and benefits appropriate to an international research organisation with a very 
collegial and family friendly working environment. The remuneration package 
comprises from a competitive salary, a comprehensive pension scheme, medical, 
educational and other social benefits, as well as financial support for 
relocation and installation, including your family and the availability of an 
excellent child care facility on campus. EMBL has a large thriving community of 
bioinformaticians, working in close collaboration with experimental scientists 
and with strong links to other local scientists and institutions.


What else you need to know

We are Europe’s flagship research laboratory for the life sciences – an 
intergovernmental organisation performing scientific research in disciplines 
including molecular biology, physics, chemistry and computer science. We are an 
international, innovative and interdisciplinary laboratory with more than 1600 
employees from many nations, operating across six sites, in Heidelberg (HQ), 
Barcelona, Hinxton near Cambridge, Hamburg, Grenoble and Rome.

Our mission is to offer vital services in training scientists, students and 
visitors at all levels; to develop new instruments and methods in the life 
sciences and actively engage in technology transfer activities, and to 
integrate European life science research.

Please note that appointments on fixed term contracts can be renewed, depending 
on circumstances at the time of the review.

Please apply online through:http://www.embl.org/jobs


For further information please contact:

Dr Dmitri Svergun, emailsvergun(at)embl-hamburg.de

Dr Clement Blanchet, emailblanchet(at)embl-hamburg.de



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