[ccp4bb] 2-year postdoctoral position

[Omid Haji-Ghassemi]

Dear 3dEM list,

A position is available for a highly motivated and skilled Post-doctoral Fellow 
(PDF) at the University of Calgary in Calgary, Alberta, Canada. The successful 
candidate will lead X-ray and potentially cryo-EM experiments to understand 
receptor complex biology and drug targeting. The position will be held within 
the Departments of Biological Sciences under the co-supervision of Dr. Matt 
(Mathilakth) Vijayan and Dr. Omid Haji-Ghassemi. 
 
The successful applicant must have a Ph.D. in structural biology or related 
fields. Excellent theoretical knowledge and practical skills in either X-ray 
crystallography or other protein biophysical methods are required. This 
includes familiarity with the expression and purification of proteins.  The 
position forms part of a collaborative, multidisciplinary effort between the 
Vijayan and Haji-Ghassemi laboratories. As such, excellent oral and written 
English communication skills, the proven ability to work and as part of a team, 
and strong individual research productivity are essential.
 
Calgary is one of the sunniest and cleanest cities in North America. and has 
been named as one of the world’s most livable cities. Hence it is a great place 
to do research and build a career while living in an affordable city. Calgary 
is about an hour drive from the majestic Rocky Mountains and Banff.  

Qualified Applicants should submit a cover letter including contact information 
for three professional references, and a curriculum vitae including a list of 
publications. Application materials should be combined into a single PDF 
document and submitted via email to omid.hajighass...@calgary.ca. 

The position is available immediately. The appointment will be at the rank of 
Postdoctoral Fellow with an annual salary of 50,000, plus benefits for two 
years, with a possible 1-year extension. Candidates are encouraged to apply for 
post-doctoral fellowships including  Eyes High program from UCalgary. 

Equity and diversity are essential to academic excellence. An open and diverse 
community fosters the inclusion of voices that have been underrepresented or 
discouraged. We encourage applications from members of groups that have been 
marginalized on any the basis of sex, sexual orientation, gender identity or 
expression, racialization, disability, political belief, religion, marital or 
family status, age, and/or status as a First Nation, Metis, Inuit, or 
Indigenous person.



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[ccp4bb] postdoctoral position at UCalgary with Omid Haji-Ghassemi and Matt (Mathilakth) Vijayan

[Omid Haji-Ghassemi]

Dear CCP4BB list,

A position is available for a highly motivated and skilled Post-doctoral Fellow 
(PDF) at the University of Calgary in Calgary, Alberta, Canada. The successful 
candidate will lead X-ray and potentially cryo-EM experiments to understand 
receptor complex biology and drug targeting. The position will be held within 
the Departments of Biological Sciences under the co-supervision of Dr. Matt 
(Mathilakth) Vijayan and Dr. Omid Haji-Ghassemi.

The successful applicant must have a Ph.D. in structural biology or related 
fields. Excellent theoretical knowledge and practical skills in either X-ray 
crystallography or other protein biophysical methods are required. This 
includes familiarity with the expression and purification of proteins.  The 
position forms part of a collaborative, multidisciplinary effort between the 
Vijayan and Haji-Ghassemi laboratories. As such, excellent oral and written 
English communication skills, the proven ability to work and as part of a team, 
and strong individual research productivity are essential.

Calgary is one of the sunniest and cleanest cities in North America. and has 
been named as one of the world’s most livable cities. Hence it is a great place 
to do research and build a career while living in an affordable city. Calgary 
is about an hour drive from the majestic Rocky Mountains and Banff. 

Qualified Applicants should submit a cover letter including contact information 
for three professional references, and a curriculum vitae including a list of 
publications. Application materials should be combined into a single PDF 
document and submitted via email to 
omid.hajighass...@calgary.ca.

The position is available immediately. The appointment will be at the rank of 
Postdoctoral Fellow with a 50,000 salary, plus benefits.

Equity and diversity are essential to academic excellence. An open and diverse 
community fosters the inclusion of voices that have been underrepresented or 
discouraged. We encourage applications from members of groups that have been 
marginalized on any the basis of sex, sexual orientation, gender identity or 
expression, racialization, disability, political belief, religion, marital or 
family status, age, and/or status as a First Nation, Metis, Inuit, or 
Indigenous person.
---
---
Omid Haji-Ghassemi, PhD
Assistant Professor
Department of Biological Sciences
University of Calgary
Libin Cardiovascular Institute
https://hajighassemilab.org




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Re: [ccp4bb] Regarding the diffraction image

[Jessica Bruhn]

Hi Kavya,

As others have mentioned, the unit cell is too small to contain your
protein. With a volume of ~4820 Ang^3, the unit cell can contain at most
~268 atoms, excluding hydrogens (divide the volume by 18 to get this
number). If the symmetry is P3, then the asymmetric unit can only contain
~89 atoms (divide the number of atoms in the unit cell by 3), which is not
a lot. It is most likely something organic from your buffers (the ligand,
TCEP, protein fragment, other buffer components, etc).

Searching the CCDC (https://www.ccdc.cam.ac.uk/structures/?) or the COD (
https://nanocrystallography.org/search.html) databases may be helpful. The
CCDC also has a unit cell searcher tool (CellCheckCSD) that you can
download and use without a license (
https://www.ccdc.cam.ac.uk/support-and-resources/downloads/).

Collecting higher resolution data (<1 Ang) and trying to solve this with
SHELXT would likely get to the bottom of things if you really want to know.

Best of luck!

Kind regards,
Jessica

On Fri, Feb 3, 2023 at 7:37 AM Artem Evdokimov 
wrote:

> With 50 mM Zn++ in solution, whatever it is will probably have a Zn salt
> in it. So if you wanted to solve it by direct methods or via SAD - that
> should do well. Sadly (hur hur) it's probably quite small, whatever it is.
>
> Artem
>
> - Cosmic Cats approve of this message
>
>
> On Fri, Feb 3, 2023 at 6:20 AM Mark J. van Raaij 
> wrote:
>
>> like others mentioned, looks like something in between a salt and a
>> protein, perhaps TCEP, the ligand, a peptide cleaved from your protein by
>> trace protease.
>> If possible, I would move the detector closer, collect an atomic
>> resolution dataset and try to solve the structure by direct methods. You
>> never know, it could be something interesting.
>>
>> Mark J van Raaij
>> Dpto de Estructura de Macromoleculas, lab 20B
>> Centro Nacional de Biotecnologia - CSIC
>> calle Darwin 3
>> E-28049 Madrid, Spain
>> tel. +34 91 585 4616 (internal 432092)
>> Section Editor Acta Crystallographica F
>> https://journals.iucr.org/f/
>> https://namedrop.io/markvanraaij
>>
>> On 3 Feb 2023, at 09:22, kavyashreem  wrote:
>>
>> Dear all,
>>
>> We crystallized a protein (30kDa) + ligand (by cocrystallization), in the
>> condition 10%PEG3350, 50mM Zinc acetate.
>>
>> Protein was in the buffer 20mM HEPES, 150mM NaCl, 1uM ZnCl2, 4mM TCEP, pH
>> 8.
>>
>> Crystal: Crystal:
>> crystal under UV m
>>
>> <8ef9453e.png>
>>
>> When we collected the data at an in-house facility, it looked something
>> like this:
>>
>> 
>>
>> The minimum resolution spot is around 9Ang and maximum ~2.2Ang.
>>
>> I have not come across a protein diffraction like this, nor of a salt.
>> When I ran the gel for the incubated protein (protein+ligand), there was no
>> degradation.
>>
>> Although, I was sure there is some problem with this image I tried
>> processing, which could not be, But indexing showed a unit cell  of 11Ang,
>> 11Ang, 46Ang in P3. which was quite expected for two of the axes but not
>> the third.
>>
>> Can anyone please shed some light on this diffraction image?
>>
>> How can it happen?
>>
>>
>> Thank you
>>
>> Regards
>>
>> Kavya
>>
>>
>> --
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>>
>>
>>
>> --
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>



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Re: [ccp4bb] small scale -15C chiller

[Tim Gruene]

Hi Artem,

the detector has four cables connected: a telephone line, a serial
line, a printer-type line, and a USB-cable. I suspect it is easier to
use the simulator, which I ordered straight away ;-)

Best,
Tim

On Fri, 3 Feb 2023 10:22:39 -0500
Artem Evdokimov  wrote:

> Hi Tim
> 
> One last option that's possibly even better, but requires rudimentary
> electronics: if you find the logic gate that flips from 0 to 1 (or
> backwards) upon thermocouple triggering below threshold temperature,
> you can simply supply +5V to the appropriate spot on the PCB, and
> Bob's your uncle.
> 
> To find the spot one has to trace the connection a bit, and have a
> handy voltmeter with a circuit probe, so when you put the TC into
> cold, it will register the signal. This assumes a fairly simple
> operation of the circuit - it may be that something much more
> sophisticated is taking place, like a signal on a CAN bus or god
> knows what else.
> 
> All the best,
> 
> Artem
> - Cosmic Cats approve of this message
> 
> 
> On Fri, Feb 3, 2023 at 2:16 AM Tim Gruene 
> wrote:
> 
> > Hi Artem,
> >
> > the simulator is exactly what I was looking for - many thanks!
> > We did build a small circuit to generate the voltage (-0.586mV for
> > -15C), but this didn't work - probably, our circuit was too simple.
> > 12V input looks energetically better to me than using a peltier
> > chiller (I meant peliter, not piezo originally...)
> >
> > Second to that I like Mark's idea of a long cable for the couple and
> > stick it in the next -20C cooler.
> >
> > And yes - I already confirmed with cooling by liquid nitrogen, that
> > the concept works: when the thermocouple indicates cold enough, I
> > can operate the diffractometer, and hence install our new alien
> > detector. I was indeed looking for a long-term solution to make
> > overnight measurements.
> >
> > Thanks to everyone. I feel overwhelmed with the large number of
> > quick responses.
> >
> > Best,
> > Tim
> >
> > On Thu, 2 Feb 2023 20:19:32 -0500
> > Artem Evdokimov  wrote:
> >  
> > > A basic Peltier element will likely work (may need a stack of two
> > > to reach -20) however the simpler option indeed would be to 'fake
> > > out' thermocouple input using a voltage, as described by Ivan.
> > >
> > > https://us.flukecal.com/Thermocouple-Temperature-Calculator
> > >
> > > And for $38 one can apparently purchase a thermocouple simulator
> > >
> > >  
> > https://www.brightwinelectronics.com/product/temperature-calibrator-k-n-thermocouple-generator-simulator
> >  
> > >
> > > Artem
> > >
> > > On Thu, Feb 2, 2023, 3:42 PM Rajkovic, Ivan <
> > > 95c2dc0d4fa4-dmarc-requ...@jiscmail.ac.uk> wrote:
> > >  
> > > > Hi Tim,
> > > >
> > > > Not sure if this would work, but can you get a voltage supply
> > > > and connect it instead of the thermocouple? You would need
> > > > something to provide a few mV:
> > > > https://www.thermocoupleinfo.com/type-k-thermocouple.htm
> > > >
> > > >
> > > > Ivan
> > > >
> > > >  
> > > > > -Original Message-
> > > > > From: CCP4 bulletin board  On Behalf
> > > > > Of Tim Gruene
> > > > > Sent: Thursday, February 02, 2023 11:57 AM
> > > > > To: CCP4BB@JISCMAIL.AC.UK
> > > > > Subject: [ccp4bb] small scale -15C chiller
> > > > >
> > > > > Good day,
> > > > >
> > > > > I would like to cool a K-type thermocouple down to -15C. The
> > > > > temperature  
> > > > does  
> > > > > not need to be very accurate, nor exactly -15C, just below
> > > > > that level.
> > > > >
> > > > > I was thinking of using a piezo-chiller, but they don't seem
> > > > > to be very  
> > > > energy  
> > > > > efficient.
> > > > >
> > > > > Could anyone make a recommendation for a simple device to cool
> > > > > the tiny thermocouple to -15C to -20C?
> > > > >
> > > > > For the details: we have an inhouse diffractometer with a dead
> > > > > detector.  
> > > > The  
> > > > > system is blocked, because the temperature of the detector
> > > > > needs to be  
> > > > below -  
> > > > > 15C. It is measured with a K-type thermocouple. I tested with
> > > > > liquid  
> > > > nitrogen.  
> > > > > The system show -64C (probably the limit of the thermocoupe)
> > > > > and I can  
> > > > operate  
> > > > > the system (and mount our new (brand-alien) detector).
> > > > >
> > > > > Thanks a lot!
> > > > >
> > > > > Best,
> > > > > Tim
> > > > >
> > > > > --
> > > > > --
> > > > > Tim Gruene
> > > > > Head of the Centre for X-ray Structure Analysis Faculty of
> > > > > Chemistry  
> > > > University  
> > > > > of Vienna
> > > > >
> > > > > Phone: +43-1-4277-70202
> > > > >
> > > > > GPG Key ID = A46BEE1A
> > > > >
> > > > > #
> > > > > ###
> > > > >
> > > > > To unsubscribe from the CCP4BB list, click the following link:
> > > > > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
> > > > >
> > > > > This message was issued to members of
> > > > > www.jiscmail.ac.uk/CCP4BB, a  
> > > > mailing  
> > 

[ccp4bb] inter-disciplinary postdoc position available

[Snyder, Greg]

A postdoctoral position is available to participate in an inter-disciplinary 
research program on biophysical studies of HIV proteins and virions at the 
Institute of Human Virology of University of Maryland School of Medicine, 
Baltimore, MD, USA. We are looking for a highly motivated candidate with a 
strong background in Biophysics, Fluorescence Microscopy, Virology, Immunology, 
and Cell Biology. This position requires experience in biophysics and 
fluorescence microscopy. Experience in Virology, immunology methods, molecular 
biology techniques, ELISA, western blotting, PCR, transfection is a plus. 
Central to our laboratory mission is an in-depth exploration of the basic 
mechanisms of humoral response to HIV-1 by biophysical methods. We are looking 
for applicants with a PhD in the fields of Biophysics, Biochemistry, or 
Immunology. If interested, please send your CV to k...@som.umaryland.edu 
(Krishanu Ray, Associate Professor, IHV, UMSOM)."







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Re: [ccp4bb] Regarding the diffraction image

[Artem Evdokimov]

With 50 mM Zn++ in solution, whatever it is will probably have a Zn salt in
it. So if you wanted to solve it by direct methods or via SAD - that should
do well. Sadly (hur hur) it's probably quite small, whatever it is.

Artem

- Cosmic Cats approve of this message


On Fri, Feb 3, 2023 at 6:20 AM Mark J. van Raaij 
wrote:

> like others mentioned, looks like something in between a salt and a
> protein, perhaps TCEP, the ligand, a peptide cleaved from your protein by
> trace protease.
> If possible, I would move the detector closer, collect an atomic
> resolution dataset and try to solve the structure by direct methods. You
> never know, it could be something interesting.
>
> Mark J van Raaij
> Dpto de Estructura de Macromoleculas, lab 20B
> Centro Nacional de Biotecnologia - CSIC
> calle Darwin 3
> E-28049 Madrid, Spain
> tel. +34 91 585 4616 (internal 432092)
> Section Editor Acta Crystallographica F
> https://journals.iucr.org/f/
> https://namedrop.io/markvanraaij
>
> On 3 Feb 2023, at 09:22, kavyashreem  wrote:
>
> Dear all,
>
> We crystallized a protein (30kDa) + ligand (by cocrystallization), in the
> condition 10%PEG3350, 50mM Zinc acetate.
>
> Protein was in the buffer 20mM HEPES, 150mM NaCl, 1uM ZnCl2, 4mM TCEP, pH
> 8.
>
> Crystal: Crystal:
> crystal under UV m
>
> <8ef9453e.png>
>
> When we collected the data at an in-house facility, it looked something
> like this:
>
> 
>
> The minimum resolution spot is around 9Ang and maximum ~2.2Ang.
>
> I have not come across a protein diffraction like this, nor of a salt.
> When I ran the gel for the incubated protein (protein+ligand), there was no
> degradation.
>
> Although, I was sure there is some problem with this image I tried
> processing, which could not be, But indexing showed a unit cell  of 11Ang,
> 11Ang, 46Ang in P3. which was quite expected for two of the axes but not
> the third.
>
> Can anyone please shed some light on this diffraction image?
>
> How can it happen?
>
>
> Thank you
>
> Regards
>
> Kavya
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>



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Re: [ccp4bb] small scale -15C chiller

[Artem Evdokimov]

Hi Tim

One last option that's possibly even better, but requires rudimentary
electronics: if you find the logic gate that flips from 0 to 1 (or
backwards) upon thermocouple triggering below threshold temperature, you
can simply supply +5V to the appropriate spot on the PCB, and Bob's your
uncle.

To find the spot one has to trace the connection a bit, and have a handy
voltmeter with a circuit probe, so when you put the TC into cold, it will
register the signal. This assumes a fairly simple operation of the
circuit - it may be that something much more sophisticated is taking place,
like a signal on a CAN bus or god knows what else.

All the best,

Artem
- Cosmic Cats approve of this message


On Fri, Feb 3, 2023 at 2:16 AM Tim Gruene  wrote:

> Hi Artem,
>
> the simulator is exactly what I was looking for - many thanks!
> We did build a small circuit to generate the voltage (-0.586mV for
> -15C), but this didn't work - probably, our circuit was too simple. 12V
> input looks energetically better to me than using a peltier chiller (I
> meant peliter, not piezo originally...)
>
> Second to that I like Mark's idea of a long cable for the couple and
> stick it in the next -20C cooler.
>
> And yes - I already confirmed with cooling by liquid nitrogen, that the
> concept works: when the thermocouple indicates cold enough, I can
> operate the diffractometer, and hence install our new alien detector. I
> was indeed looking for a long-term solution to make overnight
> measurements.
>
> Thanks to everyone. I feel overwhelmed with the large number of quick
> responses.
>
> Best,
> Tim
>
> On Thu, 2 Feb 2023 20:19:32 -0500
> Artem Evdokimov  wrote:
>
> > A basic Peltier element will likely work (may need a stack of two to
> > reach -20) however the simpler option indeed would be to 'fake out'
> > thermocouple input using a voltage, as described by Ivan.
> >
> > https://us.flukecal.com/Thermocouple-Temperature-Calculator
> >
> > And for $38 one can apparently purchase a thermocouple simulator
> >
> >
> https://www.brightwinelectronics.com/product/temperature-calibrator-k-n-thermocouple-generator-simulator
> >
> > Artem
> >
> > On Thu, Feb 2, 2023, 3:42 PM Rajkovic, Ivan <
> > 95c2dc0d4fa4-dmarc-requ...@jiscmail.ac.uk> wrote:
> >
> > > Hi Tim,
> > >
> > > Not sure if this would work, but can you get a voltage supply and
> > > connect it instead of the thermocouple? You would need something to
> > > provide a few mV:
> > > https://www.thermocoupleinfo.com/type-k-thermocouple.htm
> > >
> > >
> > > Ivan
> > >
> > >
> > > > -Original Message-
> > > > From: CCP4 bulletin board  On Behalf Of Tim
> > > > Gruene
> > > > Sent: Thursday, February 02, 2023 11:57 AM
> > > > To: CCP4BB@JISCMAIL.AC.UK
> > > > Subject: [ccp4bb] small scale -15C chiller
> > > >
> > > > Good day,
> > > >
> > > > I would like to cool a K-type thermocouple down to -15C. The
> > > > temperature
> > > does
> > > > not need to be very accurate, nor exactly -15C, just below that
> > > > level.
> > > >
> > > > I was thinking of using a piezo-chiller, but they don't seem to
> > > > be very
> > > energy
> > > > efficient.
> > > >
> > > > Could anyone make a recommendation for a simple device to cool
> > > > the tiny thermocouple to -15C to -20C?
> > > >
> > > > For the details: we have an inhouse diffractometer with a dead
> > > > detector.
> > > The
> > > > system is blocked, because the temperature of the detector needs
> > > > to be
> > > below -
> > > > 15C. It is measured with a K-type thermocouple. I tested with
> > > > liquid
> > > nitrogen.
> > > > The system show -64C (probably the limit of the thermocoupe) and
> > > > I can
> > > operate
> > > > the system (and mount our new (brand-alien) detector).
> > > >
> > > > Thanks a lot!
> > > >
> > > > Best,
> > > > Tim
> > > >
> > > > --
> > > > --
> > > > Tim Gruene
> > > > Head of the Centre for X-ray Structure Analysis Faculty of
> > > > Chemistry
> > > University
> > > > of Vienna
> > > >
> > > > Phone: +43-1-4277-70202
> > > >
> > > > GPG Key ID = A46BEE1A
> > > >
> > > > #
> > > > ###
> > > >
> > > > To unsubscribe from the CCP4BB list, click the following link:
> > > > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
> > > >
> > > > This message was issued to members of www.jiscmail.ac.uk/CCP4BB,
> > > > a
> > > mailing
> > > > list hosted by www.jiscmail.ac.uk, terms & conditions are
> > > > available at https://www.jiscmail.ac.uk/policyandsecurity/
> > >
> > >
> 
> > >
> > > To unsubscribe from the CCP4BB list, click the following link:
> > > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
> > >
> > > This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a
> > > mailing list hosted by www.jiscmail.ac.uk, terms & conditions are
> > > available at https://www.jiscmail.ac.uk/policyandsecurity/
> > >
> >
> > 

Re: [ccp4bb] Regarding the diffraction image

[Mark J. van Raaij]

like others mentioned, looks like something in between a salt and a protein, 
perhaps TCEP, the ligand, a peptide cleaved from your protein by trace protease.
If possible, I would move the detector closer, collect an atomic resolution 
dataset and try to solve the structure by direct methods. You never know, it 
could be something interesting.

Mark J van Raaij
Dpto de Estructura de Macromoleculas, lab 20B
Centro Nacional de Biotecnologia - CSIC
calle Darwin 3
E-28049 Madrid, Spain
tel. +34 91 585 4616 (internal 432092)
Section Editor Acta Crystallographica F
https://journals.iucr.org/f/
https://namedrop.io/markvanraaij

> On 3 Feb 2023, at 09:22, kavyashreem  wrote:
> 
> Dear all,
> 
> We crystallized a protein (30kDa) + ligand (by cocrystallization), in the 
> condition 10%PEG3350, 50mM Zinc acetate.
> Protein was in the buffer 20mM HEPES, 150mM NaCl, 1uM ZnCl2, 4mM TCEP, pH 8. 
> Crystal: Crystal:   
> crystal under UV m
> <8ef9453e.png>
> When we collected the data at an in-house facility, it looked something like 
> this:
> 
> The minimum resolution spot is around 9Ang and maximum ~2.2Ang. 
> I have not come across a protein diffraction like this, nor of a salt. When I 
> ran the gel for the incubated protein (protein+ligand), there was no 
> degradation.
> Although, I was sure there is some problem with this image I tried 
> processing, which could not be, But indexing showed a unit cell  of 11Ang, 
> 11Ang, 46Ang in P3. which was quite expected for two of the axes but not the 
> third.
> Can anyone please shed some light on this diffraction image?
> How can it happen?
>  
> Thank you
> Regards
> Kavya
>  
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 
> 



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[ccp4bb] Registration and abstract submission system has opened for 14th Biology and Synchrotron Radiation Conference (BSR14.com) June 11 to 14 2023 in Lund, Sweden

[Marjolein Thunnissen]

We are delighted to inform you that registration and abstract submission for 
the 14th BSR conference has opened. The meeting is being planned as a physical, 
on-site meeting, but with a virtual component to aid those who are not able to 
travel.
The International Biology and Synchrotron Radiation meetings are held every 
three years to present and discuss state-of-the-art applications in relevant 
research fields. They have a long-standing record since the first meeting in 
Frascati, Italy in 1986. Subsequent meetings were held at sites at or near the 
most advanced light source facilities around the world, with the last BSR 
meeting taking place in Shanghai, China in 2019. BSR is a unique forum to 
discuss the novel possibilities of synchrotrons and X-ray lasers and to promote 
their applications to challenging biological problems

The venue is in the city center of Lund (southern Sweden), only a 25 min train 
ride from Copenhagen Airport.

The conference will start with registration and a welcome reception on Sunday, 
June 11 2023. A three-day scientific program will follow, finishing in the 
afternoon of Wednesday, June 14, 2023. A limited number of subsidized student 
admissions is available.

For further information as well as a list of Keynote and Invited speakers, see 
www.BSR14.com.

We are very much looking forward to welcoming you in Lund in the Summer of 
2023. With kind regards

 For the BSR14 organizing team:

Marjolein Thunnissen, MAX IV
Filipe Maia, Uppsala University

[cid:3A2194AC-734C-45EB-B5A7-CE7FC0F0F1BC]


Dr. Marjolein Thunnissen
Life Science Director
MAX IV Laboratory
Lund University
P.O. Box 118, SE-221 00 Lund, Sweden
Visiting address: Fotongatan 2, 225 94 Lund
Telephone:+46 46 2224668
Mobile:  +46 766 32 04 17
www.maxiv.lu.se




[cid:3A2194AC-734C-45EB-B5A7-CE7FC0F0F1BC]


Dr. Marjolein Thunnissen
Life Science Director
MAX IV Laboratory
Lund University
P.O. Box 118, SE-221 00 Lund, Sweden
Visiting address: Fotongatan 2, 225 94 Lund
Telephone:+46 46 2224668
Mobile:  +46 766 32 04 17
www.maxiv.lu.se





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Re: [ccp4bb] Regarding the diffraction image

[Thomas Flower]

Dear Kavya,

4 mM is quite a high concentration of TCEP, perhaps they are TCEP crystals.

You could try a Unit Cell Search of the CCDC to see if you find a match: Unit 
Cell Search - WebCSD 
(cam.ac.uk)

Best,
Thomas



Thomas Flower, PhD
Senior Scientist, Protein Science

[cid:image001.png@01D937B5.E93AE6A0]

Galapagos
102 Avenue Gaston Roussel
93230 Romainville
France
T: +33 7 81 26 95 70
www.glpg.com

From: CCP4 bulletin board  On Behalf Of mesters@biochem
Sent: vendredi 3 février 2023 9:53 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Regarding the diffraction image

You don't often get email from 
mest...@biochem.uni-luebeck.de. Learn 
why this is important
A and B unit cell dimensions are hardly bigger than twice the uni cell of cubic 
NaCl and will probably not accommodate a 30 kDa protein.

Make a SDS gel of washed & dissolved crystals to be sure these are not alt or 
inhibitor crystals. You can stain the crystals with IzIt...

J.

--
Dr. math. et dis. nat. Jeroen R. Mesters
https://orcid.org/-0001-8532-6699
[cid:image002.png@01D937B5.E93AE6A0]

University of Lübeck
Institute of Biochemistry
https://www.biochem.uni-luebeck.de
phone: +49-451-3101-3105
Ratzeburger Allee 160
23562 Lübeck
Germany
--


Am 03.02.2023 um 09:22 schrieb kavyashreem 
mailto:kavyashr...@instem.res.in>>:

Dear all,
We crystallized a protein (30kDa) + ligand (by cocrystallization), in the 
condition 10%PEG3350, 50mM Zinc acetate.
Protein was in the buffer 20mM HEPES, 150mM NaCl, 1uM ZnCl2, 4mM TCEP, pH 8.
Crystal: Crystal:   crystal 
under UV m
<8ef9453e.png>
When we collected the data at an in-house facility, it looked something like 
this:

The minimum resolution spot is around 9Ang and maximum ~2.2Ang.
I have not come across a protein diffraction like this, nor of a salt. When I 
ran the gel for the incubated protein (protein+ligand), there was no 
degradation.
Although, I was sure there is some problem with this image I tried processing, 
which could not be, But indexing showed a unit cell  of 11Ang, 11Ang, 46Ang in 
P3. which was quite expected for two of the axes but not the third.
Can anyone please shed some light on this diffraction image?
How can it happen?

Thank you
Regards
Kavya



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Re: [ccp4bb] Regarding the diffraction image

[a . perrakis]

Hi Kavya,

Try https://csb.wfu.edu/tools/vmcalc/vm.html

This tells you that a 30kD protein simply does not fit the cell.

I am pretty sure you crystallised the ligand, or TCEP actually.

Also, if you look at the diffractions pattern, its clear the crystal diffracts 
beyond 1.0A, diffraction spots are really very very very strong at 2.0A.



On 3 Feb 2023, at 09:22, kavyashreem 
mailto:kavyashr...@instem.res.in>> wrote:


Dear all,

We crystallized a protein (30kDa) + ligand (by cocrystallization), in the 
condition 10%PEG3350, 50mM Zinc acetate.

Protein was in the buffer 20mM HEPES, 150mM NaCl, 1uM ZnCl2, 4mM TCEP, pH 8.

Crystal: Crystal:   crystal 
under UV m

<8ef9453e.png>

When we collected the data at an in-house facility, it looked something like 
this:



The minimum resolution spot is around 9Ang and maximum ~2.2Ang.

I have not come across a protein diffraction like this, nor of a salt. When I 
ran the gel for the incubated protein (protein+ligand), there was no 
degradation.

Although, I was sure there is some problem with this image I tried processing, 
which could not be, But indexing showed a unit cell  of 11Ang, 11Ang, 46Ang in 
P3. which was quite expected for two of the axes but not the third.

Can anyone please shed some light on this diffraction image?

How can it happen?



Thank you

Regards

Kavya





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Re: [ccp4bb] Regarding the diffraction image

[mesters@biochem]

A and B unit cell dimensions are hardly bigger than twice the uni cell of cubic 
NaCl and will probably not accommodate a 30 kDa protein.

Make a SDS gel of washed & dissolved crystals to be sure these are not alt or 
inhibitor crystals. You can stain the crystals with IzIt...

J.

--
Dr. math. et dis. nat. Jeroen R. Mesters
https://orcid.org/-0001-8532-6699



University of Lübeck
Institute of Biochemistry
https://www.biochem.uni-luebeck.de
phone: +49-451-3101-3105
Ratzeburger Allee 160
23562 Lübeck
Germany
--

> Am 03.02.2023 um 09:22 schrieb kavyashreem :
> 
> Dear all,
> 
> We crystallized a protein (30kDa) + ligand (by cocrystallization), in the 
> condition 10%PEG3350, 50mM Zinc acetate.
> Protein was in the buffer 20mM HEPES, 150mM NaCl, 1uM ZnCl2, 4mM TCEP, pH 8. 
> Crystal: Crystal:   
> crystal under UV m
> <8ef9453e.png>
> When we collected the data at an in-house facility, it looked something like 
> this:
> 
> The minimum resolution spot is around 9Ang and maximum ~2.2Ang. 
> I have not come across a protein diffraction like this, nor of a salt. When I 
> ran the gel for the incubated protein (protein+ligand), there was no 
> degradation.
> Although, I was sure there is some problem with this image I tried 
> processing, which could not be, But indexing showed a unit cell  of 11Ang, 
> 11Ang, 46Ang in P3. which was quite expected for two of the axes but not the 
> third.
> Can anyone please shed some light on this diffraction image?
> How can it happen?
>  
> Thank you
> Regards
> Kavya
>  
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 
> 



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