[ccp4bb] Job posting: Beamline Scientist at AMX, NSLS-II, BNL, NY, USA.

[Jakoncic, Jean]

Dear all,




A position of beamline scientist for the highly Automated Macromolecular 
Crystallography beamline (AMX) at the National Synchrotron Light Source II is 
currently open.



The National Synchrotron Light Source-II (NSLS-II) at Brookhaven National 
Laboratory (Upton, NY, USA) seeks a scientist to join the Structural Biology 
program that operates two state-of-the-art macromo­lecular crystallography (MX) 
beamlines, one life-sciences scattering beamline, and a cryo-EM facility. The 
successful candidate will be keen to make best scientific use of the MX 
beamlines with their micro-focus beams and high degree of automation. Our early 
experience with these cutting-edge MX beamlines shows that they have ability to 
produce usable data rapidly from crystals that gave poor diffraction elsewhere.



The principal work in the next years will be to support all aspects of the 
beamline operations and to continue developing these instruments to expand 
opportunities for structural biology research.



Position Description



The new scientist who joins this multi-national group operating cutting-edge 
instruments will bring innovation and teamwork to further the quality of X-ray 
crystallography beamlines. The successful candidate will be encouraged to 
develop opportunities for scientific collaborations that exploit the unique 
qualities of our beamlines. We would emphasize extending the mission and 
technical scope of the beamline, especially by further increasing the level of 
automation including sample centering for complex data collection and data 
processing in our high-performance computing environment. Responsibilities will 
also include interacting with the scientific user community to augment their 
scientific productivity with complementary NSLS-II life-science user programs 
and our cryo-EM facility.



Our group operates 2 state of the art MX beamlines, AMX (high throughout and 
automation) FMX (frontier experiments including serial crystallography) and LIX 
the life science scattering beamline.



AMX is a microfocus beamline with a beam size of 7x5 um2 and a flux of 4.5 1012 
ph.s-1.



AMX is a tunable beamline with a 5-18 keV range, well suited for high 
resolution data collection from large assemblies and native phasing from 
challenging samples.



AMX is equipped with a state-of-the-art robotics system, a high capacity sample 
Dewar holding up to 384 samples and an Eiger 9M detector.



Further details and how to apply can be found here:



https://jobs.bnl.gov/job/upton/beamline-scientist-highly-automated-macromolecular-crystallography-amx/3437/10947993



Please don't hesitate to get into touch for further information.



Best regards,



Jean



--

Dr. Jean Jakoncic

Lead Beamline Scientist, AMX

National Synchrotron Light Source II, Brookhaven National Laboratory

Upton, NY, 11973, USA

tel: (+1) 631 344 3930

email: jjakon...@bnl.gov



https://www.bnl.gov/ps/beamlines/beamline.php?r=17-ID-1



https://www.bnl.gov/ps/lsbr/




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Re: [ccp4bb] Semet derivative dying almost immediately in beam

[James Holton]

If it is any of these things, then we want to know about it!

Miss-alignment I doubt because the cameras on 8.2.2 are all co-axial 
(looking down the beam).  The beam size is about 1/5 the field of view, 
and the sample stays visible during the exposure.  It would be hard not 
to notice the crystal moving out of the beam.
I also doubt fluorescence scans damaging the crystal because the general 
ALS fluorescence scan protocol attenuates the incident beam by a factor 
of 1000 or more.  Few fluorescence scans give the crystal more dose than 
a single screening shot.
The cryo can be a problem, but I also doubt it in this case.  Over 20 
years, I have seen maybe 3 instances of a cryo system "burping". These 
problems are extremely difficult to detect and even more difficult to 
solve.  Hence the concern here.  Usually this happens if the neck of the 
exhaust vent gets full of ice.  Checking that is routine PM. I just 
double-checked myself and its clean.


 All of the above things are very unlikely to happen twice in a row. 
Hopefully Kimberly can grow more crystals and we can try again (with 
more than a few eyes watching everything very carefully). But right now 
I'd bet even money on equipment vs the sample.


-James Holton
MAD Scientist

On 8/30/2019 11:48 AM, Green, Todd Jason wrote:
Certainly not trying to be insulting by the suggestions but could it 
be as simple an alignment issue with the crystal, issues with the beam 
alignment or crystal damage following a  fluorescence scan? The cryo 
setup?


Like James, I’ve seen crystals decay quickly in high salts at longer 
wavelengths.


Good luck!

- Todd

Sent from my iPhone

On Aug 30, 2019, at 1:41 PM, James Holton > wrote:



That is absolutely mind-blowing.

ALS 8.2.2 has a nominal dose rate of 95 kGy/s, and you are seeing 
global damage go to completion in ~0.4s, or 40 kGy. This is 750 times 
faster than expected.  I have never heard of a cryo-cooled crystal 
decaying that fast.  This may be a new world record!  I know that is 
probably not what you wanted, but it is exciting to people like me.


Being at 4.5A is actually a good thing for radiation damage because 
features at poor resolution tend to evolve more slowly with dose than 
fine details (high-angle spots).  That is probably also not what you 
wanted, but it makes such a fast decay rate even more unusual.


I have encountered reports of extra-sensitive proteins before, but 
they always turn out to be due to something predictable, like having 
a super-high concentration of heavy atom.  For example, having 200 mM 
sodium iodide in your solvent channels will cut a typical crystal 
lifetime in half.  4 M NaI will cut it by a factor of 20, but to get 
1000x the usual decay rate you would need something like 10 M 
Ta6Br12.  And Ta6Br12 is only soluble to 2 mM.


Yes, you have Se atoms in there, but even if you have 1 in 10 
residues containing an Se atom at 0% solvent that is still only 1.0 M 
Se in the crystal.  Only enough for about a factor of 10.


I have also seen errors in beam size and flux lead to apparently 
abnormal radiation damage rates.  These can easily be as large as a 
factor of two, especially with very small beams, but it is hard to 
imagine how one could get a factor of 1000.  ALS 8.2.2 is only a few 
meters from where I'm sitting, and I'm pretty sure the flux density 
is accurate to within 20%, probably better.  I also just checked out 
the cryo stream, and it has none of the usual warning signs.


So, that leaves either a genuinely ultra-sensitive protein, or some 
kind of undetected equipment malfunction.  Either way, we at the ALS 
are very interested in this result. Would you mind trying again?  And 
let me know when you are coming?


-James Holton
MAD Scientist


On 8/29/2019 11:07 AM, Kimberly Stanek wrote:
ALS 822. I tried as low as 0.2 sec exposure but it didn't seem to 
help much.



Kimberly Stanek
Postdoctoral Researcher, Goulding Lab
Co-chair, UCI Postdoctoral Association
University of California, Irvine
Natural Science I, Room 2302
(949) 824-0014

*From:* James Holton 
*Sent:* Thursday, August 29, 2019 10:50 AM
*To:* Kimberly Stanek ; CCP4BB@JISCMAIL.AC.UK 

*Subject:* Re: [ccp4bb] Semet derivative dying almost immediately in 
beam

What exposure time are you using?  And which beamline?

-James Holton
MAD Scientist

On 8/29/2019 10:26 AM, Kimberly Stanek wrote:

Hi folks,

We have a protein that we have been trying to solve the structure 
of for a while now but so far haven't been able to get any 
diffraction better than ~4.5A. I was able to collect a full 360 
degrees of data and index, but MR is failing so we have turned to 
de novo phasing.


Recently we prepared crystals of the Semet derivative under the 
same condition. While these crystals diffracted to about the same 
resolution, I found they were dying after just one or two snaps, 
even with increased beam attenua

[ccp4bb] Post-doctoral research position in membrane protein structural biology

[Hasan, Syed Saif]

A post-doctoral research position is high-resolution structural biology of 
membrane protein complexes is available in my laboratory at the Institute for 
Bioscience and Biotechnology Research 
(IBBR;https://www.ibbr.umd.edu/profiles/s-saif-hasan) in Rockville MD. The 
post-doctoral researcher will have a choice of multiple structure-focused 
projects in cancer biology and viral pathogenesis using single particle cryoEM 
and crystallography. The researcher will have independence to guide the 
direction of their research and to pursue novel ideas should (s)he find an 
interesting scientific question related to the general research focus of my 
laboratory.

IBBR is run jointly by the University of Maryland and the National Institute of 
Standards and Technology (NIST). We are home to a large community of structural 
biologists and have extensive interactions with national laboratories and 
private companies located in the DC-Maryland area. Our new cryoEM facility 
houses a 200 keV Thermo Fisher Talos Arctica microscope equipped with a Falcon 
3 direct electron detector. Our facilities will soon be expanded to include a 
new 200 keV Thermo Fisher Glacios microscope, a Gatan K3 direct electron 
detector and a Volta phase plate. My lab works in close collaboration with 
research groups in IBBR that specialize in mass-spectrometry, computational 
biology, NMR spectroscopy, and small angle X-ray scattering.

Applicants should have experience in insect or mammalian cell culture for 
protein production. Experience in handling membrane proteins will be helpful. 
Prior training in single particle cryoEM and/or crystallography is desirable 
but not essential. If you are a membrane protein biochemist, especially with 
experience in G-proteins, and you want to explore questions in structural 
biology, this is the position for you.

Applicants who have received their PhD or MD/PhD degree should email me 
(ssha...@som.umaryland.edu) a single PDF file containing a short cover letter 
(no more than one page), a detailed curriculum vitae, contact information for 
three references, and upto 3 reprints of representative first authorship 
publication(s).

The University of Maryland, Baltimore is an Equal Opportunity, Affirmative 
Action employer. Minorities, women, individuals with disabilities and protected 
veterans are encouraged to apply.



Saif


S. Saif Hasan, PhD

Fellow, Institute for Bioscience and Biotechnology Research (IBBR), 9600 
Gudelsky Drive, Rockville, MD 20850

Assistant Professor, Department of Biochemistry and Molecular Biology, 
University of Maryland School of Medicine, 108 N. Greene St., Baltimore, MD 
21201 AND Center for Biomolecular Therapeutics (CBT), 9600 Gudelsky Drive, 
Rockville, MD 20850
Phone: 240-314-6396
Fax: 240-314-6225
https://www.ibbr.umd.edu/profiles/s-saif-hasan



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Re: [ccp4bb] Semet derivative dying almost immediately in beam

[Green, Todd Jason]

Certainly not trying to be insulting by the suggestions but could it be as 
simple an alignment issue with the crystal, issues with the beam alignment or 
crystal damage following a  fluorescence scan? The cryo setup?

Like James, I’ve seen crystals decay quickly in high salts at longer 
wavelengths.

Good luck!

- Todd

Sent from my iPhone

On Aug 30, 2019, at 1:41 PM, James Holton 
mailto:jmhol...@lbl.gov>> wrote:

That is absolutely mind-blowing.

ALS 8.2.2 has a nominal dose rate of 95 kGy/s, and you are seeing global damage 
go to completion in ~0.4s, or 40 kGy.  This is 750 times faster than expected.  
I have never heard of a cryo-cooled crystal decaying that fast.  This may be a 
new world record!  I know that is probably not what you wanted, but it is 
exciting to people like me.

Being at 4.5A is actually a good thing for radiation damage because features at 
poor resolution tend to evolve more slowly with dose than fine details 
(high-angle spots).  That is probably also not what you wanted, but it makes 
such a fast decay rate even more unusual.

I have encountered reports of extra-sensitive proteins before, but they always 
turn out to be due to something predictable, like having a super-high 
concentration of heavy atom.  For example, having 200 mM sodium iodide in your 
solvent channels will cut a typical crystal lifetime in half.  4 M NaI will cut 
it by a factor of 20, but to get 1000x the usual decay rate you would need 
something like 10 M Ta6Br12.  And Ta6Br12 is only soluble to 2 mM.

Yes, you have Se atoms in there, but even if you have 1 in 10 residues 
containing an Se atom at 0% solvent that is still only 1.0 M Se in the crystal. 
 Only enough for about a factor of 10.

I have also seen errors in beam size and flux lead to apparently abnormal 
radiation damage rates.  These can easily be as large as a factor of two, 
especially with very small beams, but it is hard to imagine how one could get a 
factor of 1000.  ALS 8.2.2 is only a few meters from where I'm sitting, and I'm 
pretty sure the flux density is accurate to within 20%, probably better.  I 
also just checked out the cryo stream, and it has none of the usual warning 
signs.

So, that leaves either a genuinely ultra-sensitive protein, or some kind of 
undetected equipment malfunction.  Either way, we at the ALS are very 
interested in this result. Would you mind trying again?  And let me know when 
you are coming?

-James Holton
MAD Scientist


On 8/29/2019 11:07 AM, Kimberly Stanek wrote:
ALS 822. I tried as low as 0.2 sec exposure but it didn't seem to help much.


Kimberly Stanek
Postdoctoral Researcher, Goulding Lab
Co-chair, UCI Postdoctoral Association
University of California, Irvine
Natural Science I, Room 2302
(949) 824-0014

From: James Holton 
Sent: Thursday, August 29, 2019 10:50 AM
To: Kimberly Stanek ; 
CCP4BB@JISCMAIL.AC.UK 

Subject: Re: [ccp4bb] Semet derivative dying almost immediately in beam

What exposure time are you using?  And which beamline?

-James Holton
MAD Scientist

On 8/29/2019 10:26 AM, Kimberly Stanek wrote:
Hi folks,

We have a protein that we have been trying to solve the structure of for a 
while now but so far haven't been able to get any diffraction better than 
~4.5A. I was able to collect a full 360 degrees of data and index, but MR is 
failing so we have turned to de novo phasing.

Recently we prepared crystals of the Semet derivative under the same condition. 
While these crystals diffracted to about the same resolution, I found they were 
dying after just one or two snaps, even with increased beam attenuation and 
decreased exposure time. I am wondering if anyone has experienced anything like 
this before and had any suggestions on what to do about it.

Thank you,



Kimberly Stanek
Postdoctoral Researcher, Goulding Lab
Co-chair, UCI Postdoctoral Association
University of California, Irvine
Natural Science I, Room 2302
(949) 824-0014



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Re: [ccp4bb] Semet derivative dying almost immediately in beam

[James Holton]

That is absolutely mind-blowing.

ALS 8.2.2 has a nominal dose rate of 95 kGy/s, and you are seeing global 
damage go to completion in ~0.4s, or 40 kGy.  This is 750 times faster 
than expected.  I have never heard of a cryo-cooled crystal decaying 
that fast.  This may be a new world record!  I know that is probably not 
what you wanted, but it is exciting to people like me.


Being at 4.5A is actually a good thing for radiation damage because 
features at poor resolution tend to evolve more slowly with dose than 
fine details (high-angle spots).  That is probably also not what you 
wanted, but it makes such a fast decay rate even more unusual.


I have encountered reports of extra-sensitive proteins before, but they 
always turn out to be due to something predictable, like having a 
super-high concentration of heavy atom.  For example, having 200 mM 
sodium iodide in your solvent channels will cut a typical crystal 
lifetime in half.  4 M NaI will cut it by a factor of 20, but to get 
1000x the usual decay rate you would need something like 10 M Ta6Br12.  
And Ta6Br12 is only soluble to 2 mM.


Yes, you have Se atoms in there, but even if you have 1 in 10 residues 
containing an Se atom at 0% solvent that is still only 1.0 M Se in the 
crystal.  Only enough for about a factor of 10.


I have also seen errors in beam size and flux lead to apparently 
abnormal radiation damage rates.  These can easily be as large as a 
factor of two, especially with very small beams, but it is hard to 
imagine how one could get a factor of 1000.  ALS 8.2.2 is only a few 
meters from where I'm sitting, and I'm pretty sure the flux density is 
accurate to within 20%, probably better.  I also just checked out the 
cryo stream, and it has none of the usual warning signs.


So, that leaves either a genuinely ultra-sensitive protein, or some kind 
of undetected equipment malfunction.  Either way, we at the ALS are very 
interested in this result. Would you mind trying again? And let me know 
when you are coming?


-James Holton
MAD Scientist


On 8/29/2019 11:07 AM, Kimberly Stanek wrote:
ALS 822. I tried as low as 0.2 sec exposure but it didn't seem to help 
much.



Kimberly Stanek
Postdoctoral Researcher, Goulding Lab
Co-chair, UCI Postdoctoral Association
University of California, Irvine
Natural Science I, Room 2302
(949) 824-0014

*From:* James Holton 
*Sent:* Thursday, August 29, 2019 10:50 AM
*To:* Kimberly Stanek ; CCP4BB@JISCMAIL.AC.UK 


*Subject:* Re: [ccp4bb] Semet derivative dying almost immediately in beam
What exposure time are you using?  And which beamline?

-James Holton
MAD Scientist

On 8/29/2019 10:26 AM, Kimberly Stanek wrote:

Hi folks,

We have a protein that we have been trying to solve the structure of 
for a while now but so far haven't been able to get any diffraction 
better than ~4.5A. I was able to collect a full 360 degrees of data 
and index, but MR is failing so we have turned to de novo phasing.


Recently we prepared crystals of the Semet derivative under the same 
condition. While these crystals diffracted to about the same 
resolution, I found they were dying after just one or two snaps, even 
with increased beam attenuation and decreased exposure time. I am 
wondering if anyone has experienced anything like this before and had 
any suggestions on what to do about it.


Thank you,



Kimberly Stanek
Postdoctoral Researcher, Goulding Lab
Co-chair, UCI Postdoctoral Association
University of California, Irvine
Natural Science I, Room 2302
(949) 824-0014



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Re: [ccp4bb] I am doing phenix refinement now. Is it a problem if the r-work and r-free values are equal?

[Tung Thanh Dinh]

Thanks, everybody. I think i fix the problem. I just either phased or autobuilt 
with the original mtz file (phaser.1.mtz)  creating new free r flags. Now the 
r-work and r-free separate (0.1859 and 0.2104 respectively).


Kindest regards,
Tung Dinh

PhD student
The University of Georgia
Department of Chemistry

From: CCP4 bulletin board  on behalf of Tristan Croll 

Sent: Friday, August 30, 2019 12:11:21 PM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: Re: [ccp4bb] I am doing phenix refinement now. Is it a problem if the 
r-work and r-free values are equal?

[External Sender]

... although this raises a question: if there are no free reflections,
then why is a "Rfree" score being reported at all?

On 2019-08-30 16:53, Christian Roth wrote:
> No.  As pointed out by Pavel, there are no reflections flagged as
> "free reflections" used to calculate Rfree. Therefore you don't get a
> real Rfree. No model bias issue etc. If you have a Rfree using ccp4
> programs, than you should used that particular original mtz in phenix.
> It should detect the flagged "free reflections" automatically.
>
> Cheers
> Christian
>
> On Fri, Aug 30, 2019 at 5:24 PM Tung Thanh Dinh 
> wrote:
>
>> I have been using elipsoidal truncated data all long. And at first i
>> couldn't find a well homologous model (50% homology is the best i
>> can find) so I use Mr Bump and Buccaneer to create a model to phase
>> and autobuild. After a lot of refinement I obtained "good" model
>> with good statistics. Then I used this "good" model to either phase
>> and autobuild again. So this may be due to the model bias?
>>
>> Kindest regards,
>> Tung Dinh
>>
>> PhD student
>> The University of Georgia
>> Department of Chemistry
>> -
>>
>> FROM: CCP4 bulletin board  on behalf of Tung
>> Thanh Dinh 
>> SENT: Friday, August 30, 2019 9:36:58 AM
>> TO: CCP4BB@JISCMAIL.AC.UK 
>> SUBJECT: [ccp4bb] I am doing phenix refinement now. Is it a problem
>> if the r-work and r-free values are equal?
>>
>> After phasing with phenix, i clicked on the phenix.refine ribbon.
>> Since then for every macrocycle of refinement, r-work and r-free
>> values are always the same. Is this a problem that I need to fix?
>>
>> Kindest regards,
>> Tung Dinh
>>
>> PhD student
>> The University of Georgia
>> Department of Chemistry
>>
>> -
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 [1]
>>
>> -
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 [1]
>
> -
>
> To unsubscribe from the CCP4BB list, click the following link:
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>
> Links:
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Re: [ccp4bb] I am doing phenix refinement now. Is it a problem if the r-work and r-free values are equal?

[Tristan Croll]

... although this raises a question: if there are no free reflections, 
then why is a "Rfree" score being reported at all?


On 2019-08-30 16:53, Christian Roth wrote:

No.  As pointed out by Pavel, there are no reflections flagged as
"free reflections" used to calculate Rfree. Therefore you don't get a
real Rfree. No model bias issue etc. If you have a Rfree using ccp4
programs, than you should used that particular original mtz in phenix.
It should detect the flagged "free reflections" automatically.

Cheers
Christian

On Fri, Aug 30, 2019 at 5:24 PM Tung Thanh Dinh 
wrote:


I have been using elipsoidal truncated data all long. And at first i
couldn't find a well homologous model (50% homology is the best i
can find) so I use Mr Bump and Buccaneer to create a model to phase
and autobuild. After a lot of refinement I obtained "good" model
with good statistics. Then I used this "good" model to either phase
and autobuild again. So this may be due to the model bias?

Kindest regards,
Tung Dinh

PhD student
The University of Georgia
Department of Chemistry
-

FROM: CCP4 bulletin board  on behalf of Tung
Thanh Dinh 
SENT: Friday, August 30, 2019 9:36:58 AM
TO: CCP4BB@JISCMAIL.AC.UK 
SUBJECT: [ccp4bb] I am doing phenix refinement now. Is it a problem
if the r-work and r-free values are equal?

After phasing with phenix, i clicked on the phenix.refine ribbon.
Since then for every macrocycle of refinement, r-work and r-free
values are always the same. Is this a problem that I need to fix?

Kindest regards,
Tung Dinh

PhD student
The University of Georgia
Department of Chemistry

-

To unsubscribe from the CCP4BB list, click the following link:
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-

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Re: [ccp4bb] I am doing phenix refinement now. Is it a problem if the r-work and r-free values are equal?

[Christian Roth]

No.  As pointed out by Pavel, there are no reflections flagged as "free
reflections" used to calculate Rfree. Therefore you don't get a real Rfree.
No model bias issue etc. If you have a Rfree using ccp4 programs, than you
should used that particular original mtz in phenix. It should detect the
flagged "free reflections" automatically.

Cheers
Christian


On Fri, Aug 30, 2019 at 5:24 PM Tung Thanh Dinh  wrote:

> I have been using elipsoidal truncated data all long. And at first i
> couldn't find a well homologous model (50% homology is the best i can find)
> so I use Mr Bump and Buccaneer to create a model to phase and autobuild.
> After a lot of refinement I obtained "good" model with good statistics.
> Then I used this "good" model to either phase and autobuild again. So this
> may be due to the model bias?
>
>
> Kindest regards,
> Tung Dinh
>
> PhD student
> The University of Georgia
> Department of Chemistry
> --
> *From:* CCP4 bulletin board  on behalf of Tung
> Thanh Dinh 
> *Sent:* Friday, August 30, 2019 9:36:58 AM
> *To:* CCP4BB@JISCMAIL.AC.UK 
> *Subject:* [ccp4bb] I am doing phenix refinement now. Is it a problem if
> the r-work and r-free values are equal?
>
>
> After phasing with phenix, i clicked on the phenix.refine ribbon. Since
> then for every macrocycle of refinement, r-work and r-free values are
> always the same. Is this a problem that I need to fix?
>
>
> Kindest regards,
> Tung Dinh
>
> PhD student
> The University of Georgia
> Department of Chemistry
>
> --
>
> 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] I am doing phenix refinement now. Is it a problem if the r-work and r-free values are equal?

[Tung Thanh Dinh]

I have been using elipsoidal truncated data all long. And at first i couldn't 
find a well homologous model (50% homology is the best i can find) so I use Mr 
Bump and Buccaneer to create a model to phase and autobuild. After a lot of 
refinement I obtained "good" model with good statistics. Then I used this 
"good" model to either phase and autobuild again. So this may be due to the 
model bias?


Kindest regards,
Tung Dinh

PhD student
The University of Georgia
Department of Chemistry

From: CCP4 bulletin board  on behalf of Tung Thanh Dinh 

Sent: Friday, August 30, 2019 9:36:58 AM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: [ccp4bb] I am doing phenix refinement now. Is it a problem if the 
r-work and r-free values are equal?


After phasing with phenix, i clicked on the phenix.refine ribbon. Since then 
for every macrocycle of refinement, r-work and r-free values are always the 
same. Is this a problem that I need to fix?



Kindest regards,
Tung Dinh

PhD student
The University of Georgia
Department of Chemistry



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Re: [ccp4bb] I am doing phenix refinement now. Is it a problem if the r-work and r-free values are equal?

[Pavel Afonine]

Thanks for sharing log file. The answer is -- there are no valid free r
flags in your data file:

Number of work/free reflections by resolution:
 work  free  %free
  bin  1: 52.1844 -  3.0380 [4249/4297]  4249 0   0.0%
  bin  2:  3.0380 -  2.4114 [3632/4074]  3632 0   0.0%
  bin  3:  2.4114 -  2.1065 [3304/4043]  3304 0   0.0%
  bin  4:  2.1065 -  1.9139 [2664/3989]  2664 0   0.0%
  bin  5:  1.9139 -  1.7767 [1763/3961]  1763 0   0.0%
  bin  6:  1.7767 -  1.6720 [1304/3975]  1304 0   0.0%
  bin  7:  1.6720 -  1.5882 [ 891/3947]   891 0   0.0%
  bin  8:  1.5882 -  1.5191 [ 571/3912]   571 0   0.0%
  bin  9:  1.5191 -  1.4606 [ 293/3936]   293 0   0.0%
  bin 10:  1.4606 -  1.4102 [ 130/3913]   130 0   0.0%
overall 18801 0   0.0%

That's what log file is for: to check for obvious issues like this one!
Pavel

On Fri, Aug 30, 2019 at 7:59 AM Pavel Afonine  wrote:

> Please send me log file off-list and that may be a start. -Thanks!
> Pavel
>
> On Fri, Aug 30, 2019 at 6:48 AM Tung Thanh Dinh  wrote:
>
>> After phasing with phenix, i clicked on the phenix.refine ribbon. Since
>> then for every macrocycle of refinement, r-work and r-free values are
>> always the same. Is this a problem that I need to fix?
>>
>>
>> Kindest regards,
>> Tung Dinh
>>
>> PhD student
>> The University of Georgia
>> Department of Chemistry
>>
>> --
>>
>> 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] I am doing phenix refinement now. Is it a problem if the r-work and r-free values are equal?

[Pavel Afonine]

Please send me log file off-list and that may be a start. -Thanks!
Pavel

On Fri, Aug 30, 2019 at 6:48 AM Tung Thanh Dinh  wrote:

> After phasing with phenix, i clicked on the phenix.refine ribbon. Since
> then for every macrocycle of refinement, r-work and r-free values are
> always the same. Is this a problem that I need to fix?
>
>
> Kindest regards,
> Tung Dinh
>
> PhD student
> The University of Georgia
> Department of Chemistry
>
> --
>
> 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] I am doing phenix refinement now. Is it a problem if the r-work and r-free values are equal?

[Tung Thanh Dinh]

It is enzyme (monomer of a small protein, 251 amino acid), not viral capsid.


Thanks.


Kindest regards,
Tung Dinh

PhD student
The University of Georgia
Department of Chemistry

From: Robbie Joosten 
Sent: Friday, August 30, 2019 10:33:44 AM
To: Tung Thanh Dinh ; CCP4BB@JISCMAIL.AC.UK 

Subject: RE: [ccp4bb] I am doing phenix refinement now. Is it a problem if the 
r-work and r-free values are equal?

[External Sender]

Well, it's not exactly normal. We could use some extra information...
Exactly the same, or just very similar? Are the values high or low? Is it a 
viral capsid?

Cheers,
Robbie

> -Original Message-
> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
> Tung Thanh Dinh
> Sent: Friday, August 30, 2019 15:37
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [ccp4bb] I am doing phenix refinement now. Is it a problem if the r-
> work and r-free values are equal?
>
> After phasing with phenix, i clicked on the phenix.refine ribbon. Since then
> for every macrocycle of refinement, r-work and r-free values are always the
> same. Is this a problem that I need to fix?
>
>
>
>
>
> Kindest regards,
> Tung Dinh
>
> PhD student
> The University of Georgia
> Department of Chemistry
>
> 
>
>
> 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] I am doing phenix refinement now. Is it a problem if the r-work and r-free values are equal?

[Robbie Joosten]

Well, it's not exactly normal. We could use some extra information...
Exactly the same, or just very similar? Are the values high or low? Is it a 
viral capsid?

Cheers,
Robbie

> -Original Message-
> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
> Tung Thanh Dinh
> Sent: Friday, August 30, 2019 15:37
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [ccp4bb] I am doing phenix refinement now. Is it a problem if the r-
> work and r-free values are equal?
> 
> After phasing with phenix, i clicked on the phenix.refine ribbon. Since then
> for every macrocycle of refinement, r-work and r-free values are always the
> same. Is this a problem that I need to fix?
> 
> 
> 
> 
> 
> Kindest regards,
> Tung Dinh
> 
> PhD student
> The University of Georgia
> Department of Chemistry
> 
> 
> 
> 
> 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] I am doing phenix refinement now. Is it a problem if the r-work and r-free values are equal?

[Tung Thanh Dinh]

After phasing with phenix, i clicked on the phenix.refine ribbon. Since then 
for every macrocycle of refinement, r-work and r-free values are always the 
same. Is this a problem that I need to fix?



Kindest regards,
Tung Dinh

PhD student
The University of Georgia
Department of Chemistry



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[ccp4bb] Crystallographer Job Opening at Fog Pharma

[Deb Conrady]

We are seeking a highly motivated Scientist to join the Structural Biology
group to structurally characterize novel compounds that target undruggable
proteins. The candidate should be a team player with a broad knowledge of
protein biochemistry and deep experience in X-Ray crystallography, a
passion for scientific research as applied to drug discovery and
development, and be eager to work in a fast-paced multidisciplinary
environment.

To learn more or apply please follow the link below:

https://grnh.se/8367ebf22



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[ccp4bb] PhD position available

[Thomas Mueller]

Structural biology/signal transduction/TGFbeta biology PhD project: Modulation 
of bone morphogenetic protein (BMP) signaling by co-receptors

Project Description

We are looking to recruit a highly motivated PhD student for a research project 
in the T.Mueller-lab at the Julius-von-Sachs Institute, University of 
Wuerzburg, Germany. 

The project deals with identification and characterization of novel 
co-receptors that interact with members of the bone morphogenetic proteins 
(BMPs) to modulate BMP signaling. The project is highly interdisciplinary and 
ranges from protein chemistry/structural biology to bone homeostasis and tissue 
regeneration. It will include bacterial and mammalian protein expression, 
crystallization studies, biochemical and biophysical analysis of the proteins 
investigated, cellular assays and high-resolution microscopy.

 

The position is fully funded for 3.5 years (50%, TV-L E13). The desired 
starting date is between 10/2019 and 01/2020. Further information on the 
research group of 

Prof. Dr. Thomas Mueller 
(https://www.biozentrum.uni-wuerzburg.de/en/bot1/research/prof-dr-thomas-mueller/
 
)
 

can be found online. 

The ideal candidate has a MSc degree in Biology/Biochemistry (or related) with 
previous MSc thesis research expertise in structure biology, and/or protein 
chemistry.

 

The University of Wuerzburg is an equal opportunity employer and particularly 
welcomes applications of qualified women and individuals with disabilities.

Applications are only accepted electronically as a single PDF file containing 
the relevant information (motivation letter, CV, A-level/BSc/MSc diplomas, 
transcripts of records, names of 2 references, and, if available, letters of 
recommendation). Please send them to the email address 
muel...@biozentrum.uni-wuerzburg.de 
. 

Applications will be continuously reviewed until the position has been filled.

 

Funding Notes

All students holding an MSc or an equivalent degree at the time of employment 
are eligible; EU and non-EU nationals are eligible.


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Re: [ccp4bb] Another difficult MR case

[Randy Read]

Dear Napoleão,

Yes, I agree with Phil that it looks like a case where there *is* translational 
NCS but it's not being used by Phaser, either because it wasn't automatically 
detected (native Patterson peak just under the default limit? more than one 
off-origin Patterson peak?) or because Phaser was told to ignore tNCS.  You 
should look in detail at the relevant section of the logfile, and manually 
override Phaser's automated decision if you think there's good evidence for 
tNCS.  I would say that, as Phil noted, the fact that two molecules are in 
basically the same orientation separated by a translation is pretty strong 
evidence.  In particular, the fact that placing the second molecule in the same 
orientation gave such a large increase in both LLG and TFZ is strong evidence: 
this tells us that having two molecules in the same orientation (even if 
they're the wrong molecule or in the wrong orientation) explains some feature 
of the data, i.e. the modulation caused by tNCS.

I'd be happy to look at the log file for you if you find it hard to interpret.

Best wishes,

Randy Read

> On 29 Aug 2019, at 17:24, Phil Jeffrey  wrote:
> 
> Are you *sure* there's no translational NCS ?
> 
> For example your first molecular replacement solution out of Phenix shows
> 
> EULER  293.6   27.7  288.7
> FRAC -0.02  0.02  0.02
> (that's "first molecule at origin in P1")
> 
> and
> 
> EULER  294.0   27.9  288.8
> FRAC -0.37  0.02  0.02
> 
> which is essentially the same orientation, and a translation down one 
> crystallographic axis (a*)
> 
> And this suggests to me that either Xtriage or Phaser is missing something 
> here.  Does Phaser find translational NCS in its initial data analysis ?  
> Unmodeled translational NCS could cause significant problems with the 
> molecular replacement search.
> 
> Phil Jeffrey
> Princeton
> 
> 
> 
> 
> On 8/29/19 11:28 AM, Napoleão wrote:
>> Deal all,
>> Sorry for the long post.
>> I have a data set obtained from a crystal produced after incubating a 
>> protease with a protein which is mostly composed by an antiparallel beta 
>> sheet. I have tried numerous approaches to solve it, and failed. Molecular 
>> replacement using Phaser, and the protease or the protein as a template 
>> yields no solution. However, molecular replacement using only part of the 
>> beta sheet yields LLG=320 TFZ==28.0 (see below).
>> The apparently good data extends to 1.9 A, as processed by XDS, and the 
>> space group is P1 (pointless agree). XDS info below:
>> SPACE_GROUP_NUMBER=1
>> UNIT_CELL_CONSTANTS=44.4372.2977.30  97.802  89.939 101.576
>>  ab  ISa
>>  9.647E-01  3.176E-03   18.07
>>  RESOLUTION NUMBER OF REFLECTIONSCOMPLETENESS R-FACTOR  R-FACTOR 
>> COMPARED I/SIGMA   R-meas  CC(1/2)  Anomal  SigAno   Nano
>>LIMIT OBSERVED  UNIQUE  POSSIBLE OF DATA   observed  expected 
>>  Corr
>>  1.90   24890   19149 23814   80.4%  58.1% 63.7%
>> 114820.77 82.2%63.8* 30.694 492
>> total  163756  125884146938   85.7%  10.6% 10.8%
>> 757443.78 15.0%99.0*-30.7615834
>> Xtriage in Phenix 1.16-3549 gives me all green lights (print below), 
>> suggesting the data presents no twinning, no translational NCS, no ice rings 
>> and is not anisotropic.
>> http://fullonline.org/science/phenix_xtriage_green.png
>> Molecular replacement in Phaser yields single solutions like:
>>Solution annotation (history):
>>SOLU SET  RFZ=3.0 TFZ=* PAK=0 LLG=29 RFZ=2.8 TFZ=8.8 PAK=1 LLG=310 
>> TFZ==27.6
>> LLG=320 TFZ==28.0
>>SOLU SPAC P 1
>>SOLU 6DIM ENSE ensemble1 EULER  293.6   27.7  288.7 FRAC -0.02  0.02  
>> 0.02 BFAC
>> -6.03
>>SOLU 6DIM ENSE ensemble1 EULER  294.0   27.9  288.8 FRAC -0.37  0.02  
>> 0.02 BFAC
>> -6.52
>>SOLU ENSEMBLE ensemble1 VRMS DELTA -0.1983 RMSD  0.49 #VRMS  0.21
>> or partial solutions like:
>>Partial Solution #1 annotation (history):
>>SOLU SET  RFZ=3.7 TFZ=* PAK=0 LLG=32 RFZ=2.8 TFZ=13.0 PAK=0 LLG=317 
>> TFZ==30.2
>> LLG=331 TFZ==30.5 RFZ=2.4 TFZ=7.2 PAK=0 LLG=464 TFZ==18.5 RFZ=2.7 
>> TFZ=5.7 PAK=1
>> LLG=501 TFZ==6.8 LLG=509 TFZ==6.6
>>SOLU SPAC P 1
>>SOLU 6DIM ENSE ensemble1 EULER   85.4  153.0  138.5 FRAC -0.01 -0.00 
>> -0.00 BFAC
>> -12.30
>>SOLU 6DIM ENSE ensemble1 EULER   86.2  153.2  139.5 FRAC -0.36 -0.01 
>> -0.01 BFAC
>> -9.16
>>SOLU 6DIM ENSE ensemble1 EULER   83.8  152.3  135.9 FRAC -0.00  0.00 
>> -0.25 BFAC
>> 1.52
>>SOLU 6DIM ENSE ensemble1 EULER  191.2  109.1   39.3 FRAC -0.27 -0.01  
>> 0.22 BFAC
>> 10.18
>>SOLU ENSEMBLE ensemble1 VRMS DELTA -0.0447 RMSD  0.49 #VRMS  0.44
>> However, after 1 refinement round in Phenix_Refine (Final: r_work = 0.4881 
>> r_free = 0.5009) I got densities that are part good and part bad, and if I 
>> delete the bad parts and refine again, the good parts become bad. Plea

[ccp4bb] PhD position available

[Jesko Koehnke]

*Neurophysiology/structural biology/microbiology PhD project: *Bacterial
infections targeting synaptic adhesion molecules: effects of bacterial
adhesin binding to adhesive components of photoreceptor/retinal synapses

*Project Description*

We are looking to recruit a highly motivated PhD student for a joint
research project between the Helmholtz Institute for Pharmaceutical
Research Saarland (HIPS, Saarbrücken, Germany - a branch of the Helmholtz
Centre for Infection Research) and Saarland Medical University (UKS,
Homburg, Germany).

The project on bacterial adhesins binding to neuronal structures is highly
interdisciplinary and ranges from molecular microbiology/structural biology
to neurophysiology and will include bacterial and mammalian protein
expression, crystallization studies, synaptic physiology using genetically
engineered reporter mice, Ca2+ imaging, cell wall associated proteome
studies, and different adhesion assays including single molecule force
spectroscopy.

The position is fully funded for 3 years (50%, TV-L E13). The desired
starting date is between 11/2019 and 02/2020. Further information on the
three research groups of

Prof. Dr. Schmitz (
https://www.uniklinikum-saarland.de/einrichtungen/fachrichtungen/anatomie_zellbiologie_und_entwicklungsbiologie/univ_prof_dr_med_frank_schmitz_anatomie/
)


Prof. Dr. Köhnke (https://www.helmholtz-hzi.de/koehnke), and

Prof. Dr. Bischoff (
https://www.uniklinikum-saarland.de/einrichtungen/kliniken_institute/infektionsmedizin/medizinische_mikrobiologie_und_hygiene/forschung/)


can be found online.

The ideal candidate has a MSc degree in Biology (or related) with previous
MSc thesis research expertise in neurophysiology, structure biology, and/or
microbiology. Willingness to routinely work under biosafety S2 level and
with mice is essential.

Applications are only accepted electronically as a single PDF file
containing the relevant information (motivation letter, CV, A-level/BSc/MSc
diplomas, transcripts of records, names of 2 references, and, if available,
letters of recommendation). Please send them to all three email addresses (
frank.schm...@uks.eu, jesko.koeh...@helmholtz-hips.de and
markus.bisch...@uks.eu) parallel. Applications will be continuously
reviewed until the position has been filled.



*Funding Notes*

All students holding an MSc or an equivalent degree at the time of
employment are eligible; EU and non-EU nationals are eligible.



*Related Subjects*

·  Medical / Clinical Science

·  Neurophysiology

·  Structural Biology

·  Microbiology

·  Molecular Biology



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[ccp4bb] Job Opening: Senior Director or Executive Director Structural Biology and Biophysics

[Fan Jiang]

Job Title: Senior Director or Executive Director Structural Biology and 
Biophysics
Viva biotech is a leading CRO organization supported by Angel investors and a 
US leading PE fund since 2008, located in Shanghai. China. Viva provides 
structure-based drug discovery, biologics and medicinal chemistry services to 
global pharmaceutical and biotech companies for their pre-clinical stage 
innovative drug development. Viva biotech is in a rapid expansion mode since 
its successful IPO on the Hong Kong Stock Exchange on May 9th, 2019. We have 
openings for senior director and executive director in structural biology and 
biochemistry. Anyone who is interested in the position, please send CV to 
h...@vivabiotech.com
 
Job Description:
We are seeking a highly motivated and innovative individual with strong working 
experiences in structure biology, biochemistry, as well as project management 
experience. The position will require leading multiple projects, working 
closely together with project managers and our partners to accomplish client 
goals successfully and timely. The candidate will be deeply involved in daily 
communications with clients and teammates via TC, emails and project meetings. 
The successful candidate is also required to build sustainable strong 
relationships with clients and external partners by active communications, 
professional conferences and on-site visits.

Key Responsibility:
The successful applicant will be responsible for the execution of the following 
tasks:
•   Provide leadership and expertise in structural biology, protein 
biochemistry, and biophysics.
•   Support and assist project managers in multiple projects of recombinant 
protein production, protein characterization and complex structure 
determination for activity-assay and structural studies.
•   Provide scientifically sound guidance, resolve and promptly response to 
any issues, problems or challenges which may arise.
•   Demonstrate strong customer and service focus. Able to thrive and 
deliver results in a fast paced, dynamic and highly multi-tasking environment.
•   Enable a positive team environment and interact with multi-disciplines 
project teams.
•   Lead a team of Cyro-EM including recruiting, on-boarding, coaching, 
business development, and performance management.
•   Understand and comply with company regulations, policies and SOPs, 
contribute to continuous improvement.
•   Candidate may periodically be asked to travel to different places in 
the US or Europe for business purpose and face-to-face meetings with clients.

Required Qualifications:
•   Doctoral degree or equivalent in structural biology, biochemistry, 
biophysics or a related field with 10+ years of industry experience
•   A proven track record of scientific achievement illustrated in your 
list of publications
•   Broad knowledge in protein production, characterization, macro 
molecular crystallography, structural biology and biophysics
•   Years of working experience in managing projects from different targets 
with clear understanding of project needs and ensuring delivery of high-quality 
data with clear communication of timeline.
•   Demonstrated ability to be flexible and adaptable to changing business 
needs and client requirements.
•   Excellent written, verbal in both English and Chinese as well as 
interpersonal communication skills is a must.
•   Strong working knowledge or familiarity with biophysical methods 
techniques such as NMR, ITC, TSA, SPR, MST, etc would be a plus.
•   Broad experience or familiarity with different aspects of structure 
determination by Cryo-EM technology including sample preparation, data 
collection, data processing using state-of-art software, and 3-D reconstruction 
would be an additional advantage.




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