Re: [ccp4bb] RFI on access to digital data

2011-11-10 Thread John R Helliwell
Dear Ashley,
Excellent find!

Within it I see that one of the UK agencies states:-
vii. What resources will you require to deliver your (Data management
and sharing) plan?

Greetings,
John


On Wed, Nov 9, 2011 at 10:50 PM, Deacon, Ashley M.
adea...@slac.stanford.edu wrote:
 I also found this interesting:

 http://www.datadryad.org/

 Ashley.

 
 From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] On Behalf Of Peter Keller 
 [pkel...@globalphasing.com]
 Sent: Wednesday, November 09, 2011 8:25 AM
 To: CCP4BB@JISCMAIL.AC.UK
 Subject: Re: [ccp4bb] RFI on access to digital data

 On Tue, 8 Nov 2011, Gerard DVD Kleywegt wrote:

 Relevant to the discussion about archiving image data:

          http://federalregister.gov/a/2011-28621


 Interesting that it quotes MIAME (minimum information about a microarray
 experiment) as an example of community-driven standardisation. When MIAME
 was being formulated, it drew in part, and learned from, the history of the
 PDB.

 It is also a field where (I am told) the raw data really are useless without
 metadata about the experiment.

 Regards,
 Peter.

 --
 Peter Keller                                     Tel.: +44 (0)1223 353033
 Global Phasing Ltd.,                             Fax.: +44 (0)1223 366889
 Sheraton House,
 Castle Park,
 Cambridge CB3 0AX
 United Kingdom




-- 
Professor John R Helliwell DSc


[ccp4bb] PhD and Post-doctoral Positions in Membrane Structural Biology at University of Freiburg

2011-11-10 Thread Carola Hunte
A post-doctoral position and a PhD position are open to study structure, 
mechanism and function of clinically relevant cation/proton antiporters and 
their integration in signalling processes. The project is part of the 
Collaborative Research Center 746 (http://www.sfb746.uni-freiburg.de) and is 
connected to the European Drug Initiative on Channels and Transporters 
(http://www.edict-project.eu). 
The Hunte research group is based at the Institute for Biochemistry and 
Molecular Biology of the University of Freiburg and is member of the BIOSS 
Centre for Biological Signalling Studies (Cluster of Excellence, 
http://www.bioss.uni-freiburg.de). Positions are available from January 2012. 
For more information, please visit the lab web site 
(http://www.biochemie.uni-freiburg.de/hunte/, go to « Research ») or contact 
Carola Hunte, to whom applications should be sent by Email.  

Prof. Dr. Carola Hunte, Institute for Biochemistry and Molecular Biology, BIOSS 
Centre for Biological Signalling Studies, University of Freiburg, Germany 
(http://www.biochemie.uni-freiburg.de/hunte/)


[ccp4bb] crystallization of synthetic peptides

2011-11-10 Thread H. Raaijmakers
Dear crystallographers,

Because of the low cost and speed of synthesizing 40- to 60-mer peptides,
I wonder whether anyone has (good or bad) experiences crystalizing such
peptides. In literature, I've found up to 34-mer synthetic coiled coils,
but no other protein class. I can imagine that a protein sample with a few
percent random deletion mutants mixed into it won't crystallize easily,
but has anyone actually tried?

cheers,

Hans


Re: [ccp4bb] crystallization of synthetic peptides

2011-11-10 Thread mjvdwoerd

 Hans,

Most natural toxins from snakes, scorpions etc are 50+/-some peptides. And 
quite a few of those have been studied and crystallized (see pdb for a list). 
Having worked on one of these structures as a graduate student, I can share my 
experience:
- Purification is harder than you would think. You are talking about  10kD, 
usually around 5kD. Many methods (size exclusion, even concentration over a 
simple membrane) don't work as easily as you would like.
- I did not have much of a problem crystallizing (i.e. no worse than other 
proteins, maybe even a little easier)
- Crystals tend to diffract well (maybe better than average)
- Structures can be hard to solve; MIR is very difficult because ions tend to 
not go into such crystals easily (because the molecules are small and tightly 
packed?); MR is hard because (again) it does not work very well on very small 
systems
- Crystallization is not necessarily purification - if you have a mixture of 
peptides to start with, it may be harder to crystallize, or not: you might get 
a crystal that is a (random-ish) mixture.
- If you have more than two cysteines in your sequence (natural toxins 
typically do), the additional problem is to get the correct folding and 
disulphide bridges; alternatively it is very hard to discriminate between 
correctly and incorrectly linked disulphides

Finally:
These sequence should be small enough for NMR. That may or may not answer your 
questions, but it avoids your original question.

Mark


 

 

-Original Message-
From: H. Raaijmakers hraaijmak...@xs4all.nl
To: CCP4BB CCP4BB@JISCMAIL.AC.UK
Sent: Thu, Nov 10, 2011 8:16 am
Subject: [ccp4bb] crystallization of synthetic peptides


Dear crystallographers,

Because of the low cost and speed of synthesizing 40- to 60-mer peptides,
I wonder whether anyone has (good or bad) experiences crystalizing such
peptides. In literature, I've found up to 34-mer synthetic coiled coils,
but no other protein class. I can imagine that a protein sample with a few
percent random deletion mutants mixed into it won't crystallize easily,
but has anyone actually tried?

cheers,

Hans

 


Re: [ccp4bb] crystallization of synthetic peptides

2011-11-10 Thread George Sheldrick
As Mark says, structure solution of smallish peptides is not usually as 
easy as one might expect. A number of the small (say up to 50 residue) 
peptides in the PDB were solved by direct methods, but these require 
native data to 1.2A or (preferably) better. If sulfur is present in the 
molecule, SAD is a good choice and does not require such a very high 
resolution, but you need highly redundant data, so a high symmetry space 
group helps. If even one Met is present in the sequence, since you are 
synthesizing the peptides anyway, you can replace it with selenomethionine.


George

On 11/10/2011 09:15 PM, mjvdwo...@netscape.net wrote:

Hans,

Most natural toxins from snakes, scorpions etc are 50+/-some peptides. 
And quite a few of those have been studied and crystallized (see pdb 
for a list). Having worked on one of these structures as a graduate 
student, I can share my experience:
- Purification is harder than you would think. You are talking about  
10kD, usually around 5kD. Many methods (size exclusion, even 
concentration over a simple membrane) don't work as easily as you 
would like.
- I did not have much of a problem crystallizing (i.e. no worse than 
other proteins, maybe even a little easier)

- Crystals tend to diffract well (maybe better than average)
- Structures can be hard to solve; MIR is very difficult because ions 
tend to not go into such crystals easily (because the molecules are 
small and tightly packed?); MR is hard because (again) it does not 
work very well on very small systems
- Crystallization is not necessarily purification - if you have a 
mixture of peptides to start with, it may be harder to crystallize, or 
not: you might get a crystal that is a (random-ish) mixture.
- If you have more than two cysteines in your sequence (natural toxins 
typically do), the additional problem is to get the correct folding 
and disulphide bridges; alternatively it is very hard to discriminate 
between correctly and incorrectly linked disulphides


Finally:
These sequence should be small enough for NMR. That may or may not 
answer your questions, but it avoids your original question.


Mark



-Original Message-
From: H. Raaijmakers hraaijmak...@xs4all.nl
To: CCP4BB CCP4BB@JISCMAIL.AC.UK
Sent: Thu, Nov 10, 2011 8:16 am
Subject: [ccp4bb] crystallization of synthetic peptides

Dear crystallographers,

Because of the low cost and speed of synthesizing 40- to 60-mer peptides,
I wonder whether anyone has (good or bad) experiences crystalizing such
peptides. In literature, I've found up to 34-mer synthetic coiled coils,
but no other protein class. I can imagine that a protein sample with a few
percent random deletion mutants mixed into it won't crystallize easily,
but has anyone actually tried?

cheers,

Hans




Re: [ccp4bb] How to calculate the percent of the buried hydrohobic surface area in a protein with known structure

2011-11-10 Thread Cale Dakwar
Jiyuan,

I believe PISA will easily do this for you.

C



On Thu, Nov 10, 2011 at 5:10 PM, Ke, Jiyuan jiyuan...@vai.org wrote:

 Dear All,

 ** **

 I have a protein that exists as a dimer in the crystal structure. I want
 to calculate and compare the area of the buried hydrophobic core of a
 monomer with that of a dimer? Does anyone know how to do this?  Thanks in
 advance!

 ** **

 Jiyuan Ke, Ph.D.

 Research Scientist

 Van Andel Research Institute

 333 Bostwick Ave NE

 Grand Rapids, MI 49503

 ** **
  --
  *The information transmitted is intended only for the person or entity
 to which it is addressed and may contain confidential and/or privileged
 material. Any review, retransmission, dissemination or other use of, or
 taking of any action in reliance upon, this information by persons or
 entities other than the intended recipient is prohibited. If you received
 this in error, please contact the sender and delete the material from any
 computer.*
 --



[ccp4bb] Web Seminar: Home Lab SAD phasing with HKL-3000: From data collection to refined models in less than an hour

2011-11-10 Thread Angela Criswell
Dear colleagues,

I would like to draw your attention to an upcoming free, educational webinar
to be presented by Jim Pflugrath, Ph. D. titled Home Lab SAD phasing with
HKL-3000: From data collection to refined models in less than an hour. This
interactive tutorial and webinar will demonstrate how to use HKL-3000 to
process diffraction images, find the anomalous substructure with SHELXD,
phase with SHELXC, MLPHARE, and DM, then build with ARP/wARP and refine with
REFMAC (Kudos to all the authors of these programs!). Emphasis will be on
practical tips and how to interpret the output. Relatively low redundancy
diffraction datasets will be used as examples to dispel some of the myths
about sulfur and selenium Home Lab SAD phasing.

This webinar is scheduled to occur on Thursday, November 17th 10:00 AM CST
(8:00 AM PST / 4:00 PM GMT). You can find more information, including a
registration link at: http://www.rigaku.com/protein/webinars.html.

Best regards,
Angela


NOTE: You can watch some of our past webinars at:
http://www.rigaku.com/protein/webinars-past.html. This list of webinars
includes educational topics, such as data processing with d*TREK, mosflm,
XDS and HKL as well as topics on diffraction data collection. Also, don't
miss the great talks and historical perspectives from industry experts such
as Michael Rossmann, Brian Matthews and Ian Wilson.
 
-- 
Angela R. Criswell, Ph. D.
Rigaku Americas Corporation
9009 New Trails Drive
The Woodlands, TX 77381 USA
Ph: +1 281 362 2300  ext. 216
Fax: +1 281 364 3628
Email: angela.crisw...@rigaku.com
URL: http://www.rigaku.com






[ccp4bb] effect of Izit dye within the crystal structure

2011-11-10 Thread adam andres



Hi crystallographers

Has anyone actually collected data on a crystal that
has been treated with Izit dye? If so did you
see any structural effects or know any structure that presentthis dye? 

Cheers

Adam Campos

Re: [ccp4bb] effect of Izit dye within the crystal structure

2011-11-10 Thread Bosch, Juergen
I wouldn't be surprised if it is methylene blue.
Jürgen

On Nov 10, 2011, at 11:34 PM, adam andres wrote:



Hi crystallographers


Has anyone actually collected data on a crystal that
has been treated with Izit dye? If so did you
see any structural effects or know any structure that present this dye?

Cheers

Adam Campos


..
Jürgen Bosch
Johns Hopkins University
Bloomberg School of Public Health
Department of Biochemistry  Molecular Biology
Johns Hopkins Malaria Research Institute
615 North Wolfe Street, W8708
Baltimore, MD 21205
Office: +1-410-614-4742
Lab:  +1-410-614-4894
Fax:  +1-410-955-2926
http://web.mac.com/bosch_lab/







Re: [ccp4bb] crystallization of synthetic peptides

2011-11-10 Thread Joel Tyndall
Some HIV protease structures have been done using synthetic HIV protease (99 
amino acid monomers). Look at J. Martin et al from UQ in Queensland. I believe 
this was done with Steve Kent. The protein contains some non-natural amino 
acids too.

Hope this helps

-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of H. 
Raaijmakers
Sent: Friday, 11 November 2011 4:17 a.m.
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] crystallization of synthetic peptides

Dear crystallographers,

Because of the low cost and speed of synthesizing 40- to 60-mer peptides, I 
wonder whether anyone has (good or bad) experiences crystalizing such peptides. 
In literature, I've found up to 34-mer synthetic coiled coils, but no other 
protein class. I can imagine that a protein sample with a few percent random 
deletion mutants mixed into it won't crystallize easily, but has anyone 
actually tried?

cheers,

Hans