Re: [ccp4bb] protein quasicrystals?

[Gyanendra Kumar]

Hi Yu,

Have you tried using the Additive Screen (e.g. from Hampton Research) on
top of your crystallization condition, and varying the ratio between
protein complex and crystallization solution? From the diffraction pattern,
it looks you are almost there. Salt crystals don't show spots close to the
beam stop usually, so the chance of them being salt crystals is negligible.
A little bit of tweaking in crystallization conditions should do the trick.
If all this fails, probably, you will have to remove any floppy ends from
the proteins in the new constructs.
I had a similar experience where the protein with His-tag showed crystals
in a lot of conditions but all spherical and cylindrical crystals
diffracting to 3.5 A. The protein after removing the His-tag gave crystals
that diffracted to 2.4 A.

Good luck!
-Gyan

On Tue, Feb 13, 2018 at 9:09 AM, Yu Qiu  wrote:

> Hi,
>
>
>
> I have been trying to crystallize a protein complex and keep getting
> sphere shape crystals. The diffraction is around 3 angstrom, but looks like
> multiple lattices. I am wondering if it could be a quasi crystal? Is there
> anyone has such experience?
>
>
>
> Thanks,
>
> Yu
>



-- 
Gyanendra Kumar, PhD
Associate Scientist,
St. Jude Children's Research Hospital,
Department of Structural Biology,
262, Danny Thomas Place, MS-311
Memphis, TN 38105
Cell: 631-875-9189
https://www.linkedin.com/in/gyanendrakumar
https://scholar.google.com/gyanendrakumar

https://www.researchgate.net/profile/Gyanendra_Kumar3
http://stjude.academia.edu/GyanendraKumar
---

Re: [ccp4bb] protein quasicrystals?

[Diana Tomchick]

Some of the high intensity, high resolution spots are possibly from ice.

Diana

**
Diana R. Tomchick
Professor
Departments of Biophysics and Biochemistry
University of Texas Southwestern Medical Center
5323 Harry Hines Blvd.
Rm. ND10.214A
Dallas, TX 75390-8816
diana.tomch...@utsouthwestern.edu
(214) 645-6383 (phone)
(214) 645-6353 (fax)

On Feb 13, 2018, at 3:09 PM, Keller, Jacob 
mailto:kell...@janelia.hhmi.org>> wrote:

I would say definitely not a quasicrystal, just multiple crystals, but the 
spots look like salt spots to me, being very sharp and intense. The puzzling 
thing is that the low-resolution zone is so populated, which would argue a bit 
against salt.

JPK

+
Jacob Pearson Keller
Research Scientist / Looger Lab
HHMI Janelia Research Campus
19700 Helix Dr, Ashburn, VA 20147
Desk: (571)209-4000 x3159
Cell: (301)592-7004
+

The content of this email is confidential and intended for the recipient 
specified in message only. It is strictly forbidden to share any part of this 
message with any third party, without a written consent of the sender. If you 
received this message by mistake, please reply to this message and follow with 
its deletion, so that we can ensure such a mistake does not occur in the future.

From: yu@sanofi.com [mailto:yu@sanofi.com]
Sent: Tuesday, February 13, 2018 4:03 PM
To: Keller, Jacob mailto:kell...@janelia.hhmi.org>>; 
CCP4BB@JISCMAIL.AC.UK
Subject: RE: [ccp4bb] protein quasicrystals?

As asked by a few people, here are the images of crystals and diffraction.

Thanks,
Yu

From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Keller, 
Jacob
Sent: Tuesday, February 13, 2018 4:00 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [EXTERNAL] Re: [ccp4bb] protein quasicrystals?

I also would love to see an image….

JPK

+
Jacob Pearson Keller
Research Scientist / Looger Lab
HHMI Janelia Research Campus
19700 Helix Dr, Ashburn, VA 20147
Desk: (571)209-4000 x3159
Cell: (301)592-7004
+

The content of this email is confidential and intended for the recipient 
specified in message only. It is strictly forbidden to share any part of this 
message with any third party, without a written consent of the sender. If you 
received this message by mistake, please reply to this message and follow with 
its deletion, so that we can ensure such a mistake does not occur in the future.

From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of James 
Phillips
Sent: Tuesday, February 13, 2018 3:03 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] protein quasicrystals?

There are programs which are good at indexing patterns from multiply twinned 
crystals. Bruker AXS has one, to my knowledge. There may be other sources. I 
suggest you try that first before you invoke a quasicrystal explanation.




James Phillips

On Tue, Feb 13, 2018 at 12:07 PM, Takanori Nakane 
mailto:tnak...@mrc-lmb.cam.ac.uk>> wrote:
Hi,

"dials.reciprocal_space_viewer" is very useful to identify multiple lattices.
For quasicrystal and modulated crystals, "dials.rs_mapper" is also very
useful.

Best regards,

Takanori Nakane

> Have you tried microseeding of these sphere crystals? It may help to get
> better crystals.
>
>
> Burak
>
> 
> From: CCP4 bulletin board 
> mailto:CCP4BB@JISCMAIL.AC.UK>> on behalf of Yu Qiu
> mailto:yu@sanofi.com>>
> Sent: 13 February 2018 15:09:43
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [ccp4bb] protein quasicrystals?
>
>
> Hi,
>
>
>
> I have been trying to crystallize a protein complex and keep getting
> sphere shape crystals. The diffraction is around 3 angstrom, but looks
> like multiple lattices. I am wondering if it could be a quasi crystal? Is
> there anyone has such experience?
>
>
>
> Thanks,
>
> Yu
>




UT Southwestern


Medical Center



The future of medicine, today.

Re: [ccp4bb] protein quasicrystals?

[Keller, Jacob]

I would say definitely not a quasicrystal, just multiple crystals, but the 
spots look like salt spots to me, being very sharp and intense. The puzzling 
thing is that the low-resolution zone is so populated, which would argue a bit 
against salt.

JPK

+
Jacob Pearson Keller
Research Scientist / Looger Lab
HHMI Janelia Research Campus
19700 Helix Dr, Ashburn, VA 20147
Desk: (571)209-4000 x3159
Cell: (301)592-7004
+

The content of this email is confidential and intended for the recipient 
specified in message only. It is strictly forbidden to share any part of this 
message with any third party, without a written consent of the sender. If you 
received this message by mistake, please reply to this message and follow with 
its deletion, so that we can ensure such a mistake does not occur in the future.

From: yu@sanofi.com [mailto:yu@sanofi.com]
Sent: Tuesday, February 13, 2018 4:03 PM
To: Keller, Jacob ; CCP4BB@JISCMAIL.AC.UK
Subject: RE: [ccp4bb] protein quasicrystals?

As asked by a few people, here are the images of crystals and diffraction.

Thanks,
Yu

From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Keller, 
Jacob
Sent: Tuesday, February 13, 2018 4:00 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [EXTERNAL] Re: [ccp4bb] protein quasicrystals?

I also would love to see an image….

JPK

+
Jacob Pearson Keller
Research Scientist / Looger Lab
HHMI Janelia Research Campus
19700 Helix Dr, Ashburn, VA 20147
Desk: (571)209-4000 x3159
Cell: (301)592-7004
+

The content of this email is confidential and intended for the recipient 
specified in message only. It is strictly forbidden to share any part of this 
message with any third party, without a written consent of the sender. If you 
received this message by mistake, please reply to this message and follow with 
its deletion, so that we can ensure such a mistake does not occur in the future.

From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of James 
Phillips
Sent: Tuesday, February 13, 2018 3:03 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] protein quasicrystals?

There are programs which are good at indexing patterns from multiply twinned 
crystals. Bruker AXS has one, to my knowledge. There may be other sources. I 
suggest you try that first before you invoke a quasicrystal explanation.




James Phillips

On Tue, Feb 13, 2018 at 12:07 PM, Takanori Nakane 
mailto:tnak...@mrc-lmb.cam.ac.uk>> wrote:
Hi,

"dials.reciprocal_space_viewer" is very useful to identify multiple lattices.
For quasicrystal and modulated crystals, "dials.rs_mapper" is also very
useful.

Best regards,

Takanori Nakane

> Have you tried microseeding of these sphere crystals? It may help to get
> better crystals.
>
>
> Burak
>
> 
> From: CCP4 bulletin board 
> mailto:CCP4BB@JISCMAIL.AC.UK>> on behalf of Yu Qiu
> mailto:yu@sanofi.com>>
> Sent: 13 February 2018 15:09:43
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [ccp4bb] protein quasicrystals?
>
>
> Hi,
>
>
>
> I have been trying to crystallize a protein complex and keep getting
> sphere shape crystals. The diffraction is around 3 angstrom, but looks
> like multiple lattices. I am wondering if it could be a quasi crystal? Is
> there anyone has such experience?
>
>
>
> Thanks,
>
> Yu
>

Re: [ccp4bb] protein quasicrystals?

[Keller, Jacob]

I also would love to see an image….

JPK

+
Jacob Pearson Keller
Research Scientist / Looger Lab
HHMI Janelia Research Campus
19700 Helix Dr, Ashburn, VA 20147
Desk: (571)209-4000 x3159
Cell: (301)592-7004
+

The content of this email is confidential and intended for the recipient 
specified in message only. It is strictly forbidden to share any part of this 
message with any third party, without a written consent of the sender. If you 
received this message by mistake, please reply to this message and follow with 
its deletion, so that we can ensure such a mistake does not occur in the future.

From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of James 
Phillips
Sent: Tuesday, February 13, 2018 3:03 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] protein quasicrystals?

There are programs which are good at indexing patterns from multiply twinned 
crystals. Bruker AXS has one, to my knowledge. There may be other sources. I 
suggest you try that first before you invoke a quasicrystal explanation.




James Phillips

On Tue, Feb 13, 2018 at 12:07 PM, Takanori Nakane 
mailto:tnak...@mrc-lmb.cam.ac.uk>> wrote:
Hi,

"dials.reciprocal_space_viewer" is very useful to identify multiple lattices.
For quasicrystal and modulated crystals, "dials.rs_mapper" is also very
useful.

Best regards,

Takanori Nakane

> Have you tried microseeding of these sphere crystals? It may help to get
> better crystals.
>
>
> Burak
>
> 
> From: CCP4 bulletin board 
> mailto:CCP4BB@JISCMAIL.AC.UK>> on behalf of Yu Qiu
> mailto:yu@sanofi.com>>
> Sent: 13 February 2018 15:09:43
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [ccp4bb] protein quasicrystals?
>
>
> Hi,
>
>
>
> I have been trying to crystallize a protein complex and keep getting
> sphere shape crystals. The diffraction is around 3 angstrom, but looks
> like multiple lattices. I am wondering if it could be a quasi crystal? Is
> there anyone has such experience?
>
>
>
> Thanks,
>
> Yu
>

Re: [ccp4bb] protein quasicrystals?

[James Phillips]

There are programs which are good at indexing patterns from multiply
twinned crystals. Bruker AXS has one, to my knowledge. There may be other
sources. I suggest you try that first before you invoke a quasicrystal
explanation.




James Phillips

On Tue, Feb 13, 2018 at 12:07 PM, Takanori Nakane  wrote:

> Hi,
>
> "dials.reciprocal_space_viewer" is very useful to identify multiple
> lattices.
> For quasicrystal and modulated crystals, "dials.rs_mapper" is also very
> useful.
>
> Best regards,
>
> Takanori Nakane
>
> > Have you tried microseeding of these sphere crystals? It may help to get
> > better crystals.
> >
> >
> > Burak
> >
> > 
> > From: CCP4 bulletin board  on behalf of Yu Qiu
> > 
> > Sent: 13 February 2018 15:09:43
> > To: CCP4BB@JISCMAIL.AC.UK
> > Subject: [ccp4bb] protein quasicrystals?
> >
> >
> > Hi,
> >
> >
> >
> > I have been trying to crystallize a protein complex and keep getting
> > sphere shape crystals. The diffraction is around 3 angstrom, but looks
> > like multiple lattices. I am wondering if it could be a quasi crystal? Is
> > there anyone has such experience?
> >
> >
> >
> > Thanks,
> >
> > Yu
> >
>

Re: [ccp4bb] protein quasicrystals?

[Takanori Nakane]

Hi,

"dials.reciprocal_space_viewer" is very useful to identify multiple lattices.
For quasicrystal and modulated crystals, "dials.rs_mapper" is also very
useful.

Best regards,

Takanori Nakane

> Have you tried microseeding of these sphere crystals? It may help to get
> better crystals.
>
>
> Burak
>
> 
> From: CCP4 bulletin board  on behalf of Yu Qiu
> 
> Sent: 13 February 2018 15:09:43
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [ccp4bb] protein quasicrystals?
>
>
> Hi,
>
>
>
> I have been trying to crystallize a protein complex and keep getting
> sphere shape crystals. The diffraction is around 3 angstrom, but looks
> like multiple lattices. I am wondering if it could be a quasi crystal? Is
> there anyone has such experience?
>
>
>
> Thanks,
>
> Yu
>

Re: [ccp4bb] protein quasicrystals?

[Kabasakal, Burak V]

Have you tried microseeding of these sphere crystals? It may help to get better 
crystals.


Burak


From: CCP4 bulletin board  on behalf of Yu Qiu 

Sent: 13 February 2018 15:09:43
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] protein quasicrystals?


Hi,



I have been trying to crystallize a protein complex and keep getting sphere 
shape crystals. The diffraction is around 3 angstrom, but looks like multiple 
lattices. I am wondering if it could be a quasi crystal? Is there anyone has 
such experience?



Thanks,

Yu

[ccp4bb] Research Technician Vanderbilt University.

[Spiller, Benjamin]

Colleagues,
The Spiller lab in the Department of Pharmacology at Vanderbilt University is 
seeking a Research Assistant to assist Dr. Professor Spiller in his laboratory. 
The Spiller lab is a structural biology lab focused on infectious disease and 
the host’s immune response. The job requires a moderate ability to work 
independently but also involves working directly with Dr. Spiller and other lab 
members to help determine crystal structures. The candidate will be expected to 
interact professionally with other lab members. Preference will be given to 
applicants with experience in some of the following responsibilities.
Molecular Biology

  *   Design and create new protein constructs for crystallization trials.
  *   Optimize protein expression of new protein constructs.
Protein Purification

  *   Design and carry out experiments on the basis of discussed plans with Dr. 
Spiller
  *   Analyze chromatography experiments.
Crystallization

  *   Design and carry out high throughput crystallization trials
  *   Optimize crystallization conditions

Interested applicants should send a CV and cover letter to Ben Spiller.

benjamin.spil...@vanderbilt.edu





Ben Spiller
Associate Professor
Departments of Pharmacology
and Pathology, Microbiology, and Immunology
Vanderbilt University School of Medicine
office:  615-322-6766

Re: [ccp4bb] protein quasicrystals?

[Gloria Borgstahl]

I am very interested in this topic, and have found incommensurately
modulated crystals and few examples of possible protein quasicrystals.
Do you have any images you could share?

On Tue, Feb 13, 2018 at 9:09 AM, Yu Qiu  wrote:
> Hi,
>
>
>
> I have been trying to crystallize a protein complex and keep getting sphere
> shape crystals. The diffraction is around 3 angstrom, but looks like
> multiple lattices. I am wondering if it could be a quasi crystal? Is there
> anyone has such experience?
>
>
>
> Thanks,
>
> Yu

[ccp4bb] protein quasicrystals?

[Yu Qiu]

Hi,

I have been trying to crystallize a protein complex and keep getting sphere 
shape crystals. The diffraction is around 3 angstrom, but looks like multiple 
lattices. I am wondering if it could be a quasi crystal? Is there anyone has 
such experience?

Thanks,
Yu

[ccp4bb] PhD Positions in Integrative Structural Biology in Vienna

[Kristina Djinovic Carugo]

*International PhD Program in
**Integrative Structural Biology (ISB)*

*www.phd-structural-biology.at
invites applications for**PhD studentships **

***

The ISB Program offers a unique training and research network to study 
the structure and mechanism of complex macro-molecular systems involved 
in fundamental biological processes, including muscle development, lipid 
activated signal transduction, and protein-nucleic acids interactions.


The ISB Program integrates state-of-the-art structural, functional and 
computational biology approaches with an emphasis on the implementation 
of hybrid structural biology methods. We offer challenging, 
interdisciplinary PhD projects, an innovative research-based training 
and mentoring program and a supportive, collaborative research 
environment. The working language for research and teaching is English.


Highly motivated students with a strong interest in Structural and/or 
Computational Biology are welcome to apply. PhD applicants should have 
an academic degree equivalent to a Diploma or a Masters in Biochemistry, 
Biophysics, Chemistry, Computational Biology or related disciplines 
and**should**be able to communicate in English at an advanced level.


Interested candidates are invited to visit the home pages of the teams 
of the International PhD program in Integrative Structural Biology 
at:www.mfpl.ac.at 
/training/phd-opportunities/doctoral-program-structural-biology.html 



Students will receive a monthly salary according to the scales of the 
Austrian Science Fund FWF. At present, this is 2000 € per month before 
deductions for tax, health insurance and pension contributions.


Apply 
at:http://www.mfpl.ac.at/training/phd-opportunities/how-to-apply.html(*Deadline: 
8^th March 2018*).


--
Department of Structural and Computational Biology
Max F. Perutz Laboratories
University of Vienna
Vienna Biocenter (VBC), Campus Vienna Biocenter 5
A-1030 Vienna
Austria


e-mail: kristina.djino...@univie.ac.at
Phone: +43-1-4277-52203
Phone: +43-1-4277-52201 (secretary)
Mobile A: +43-664-602 77-522 03
Fax: +43-1-4277-9522