[ccp4bb] ICCBM12 conference , Cancun Mexico

[mesters]

Dear collegues,

I would like to bring to your attention *ICCBM12*, the 12th 
International Conference on the Crystallization of Biological 
Macromolecules, that will take place in Cancún, Mexico (May 6-9, 2008). 
The conference will be preceded by two day, hands on, crystallization 
workshop.


Please visit the website for more details: 
http:/www.iquimica.unam.mx/ICCBM12 


- Jeroen -
IOBCr secretary
http://www.iobcr.org/

Re: [ccp4bb] AW: [ccp4bb] removal of sulfate ion from the active site

[Marius Schmidt]

Exactly, solving the equation is necessary to estimate the
required concentration
Set up the eqn., use large volume (1mL) for soaking solution and
small volume (1microL) for the crystal: therefore C(free) ~ C(total),
simplify, solve for bound ligand in crystal. Thats all.
And I can tell you: stoichiometry plus a few times the Kd is 
usually NOT sufficient. Just calculate it.

M

> In those old chemical kinetics courses it was explicitly or
> implicitly clear that [I] refers to I(free), not I(total).
> The way assays are usually run, [E]< approximation the amount of bound ligand is negligible.
> 
> The way we set up crystallization, [E] is often mM
> while K(I) is uM or below, and you had better consider
> concentration AND total amount. You will never get
> decent occupancy if you add 1 uM ligand to 1 mM protein,
> even if the K(I) is 10 nM! On the other hand if you
> ignore K(I) and add stoichiometric ligand, dissociation
> of a few time K(I) to satisfy the free concentration
> will not hurt occupancy significantly.
> If you add 2x stoichiometric to
> be safe, you may also fill some very low affinity
> (100 uM) site. Use stoichiometric pus a few x Kd,
> or solve quadratic equation to see how much is
> really required.
> 
> Marius Schmidt wrote:
> 
>> think about your old chemical kinetics courses.
>> what counts is concentration and not amount.
>> 
>> M
>> 
>> 
>>>Dear Marius and others,
>>>here I would like to comment: The problem with soaking is often not
>>>so much the concentration of the ligand, but the amount of ligand
>>>needed to fill all binding sites in the crystal. A typical crystal
>>>contains about 20 mM protein so one has to add the equivalent amount
>>>of ligand. On the other hand, the concentration UNBOUND inhibitor,
>>>asuming a 1:1 protein-ligand complex, need only to be in the order of
>>>10-100 times the Kd (90-99% occupancy). Ways to overcome this is to
>>>soak in a large volume of mother liquor (containing a large amount of
>>>ligand) or to add solid ligand to the mother liquor and let the
>>>ligand slowly dissolve and diffuse into the crystal.
>>>
>>>Herman
>>>

PD Dr. habil. Marius Schmidt
Physikdepartment E17
Technische Universitaet Muenchen
James Franck Strasse
85747 Garching/Germany
email: [EMAIL PROTECTED]
http://users.physik.tu-muenchen.de/marius/
phone: +49-(0)89-2891-2550
fax:   +49-(0)89-2891-2548

[ccp4bb] Stereo glass with LCD monitor...

[Subramanian Karthikeyan]

Dear Members,

We recently purchased a DELL graphics workstation with LCD monitor
(17"). Till now I had assumption that stereo glass will not work on
LCD monitors and it needs CRT monitors. But a company with in the
following link

https://edimensional.com/product_info.php?cPath=21&products_id=28&osCsid=05b9a226d02dbc81a80115e5c7bdf77c

claims that they can sell wireless stereo 3D glass for LCD monitor and
it costs $100 only.

I would like to know if anybody has an idea about this glass and the
performance of this for crystallographic work (O, pymol, etc).

Thanking you

Sincerely
Karthikeyan S.

[ccp4bb] Bernal Symposium. Dublin, Ireland. 3 -4 September 2007

[Martin.Caffrey]

Bernal Symposium.  Structural Biology

 

Dublin, Ireland

 

3 - 4 September 2007

 

 

A symposium to honour the many contributions of J. D. Bernal (1901-1971)
to structural biology will be held in Dublin, Ireland, 3rd and 4th
September, 2007.  Among the participants are individuals who knew or
worked directly with Bernal as well as a select group of structural
biologists with an interest in biomembranes.   Confirmed speakers
include J. Watson (CSHL), K. Holmes (MPI Heidelberg), M. Rossmann
(Purdue), R. Stroud (UCSF), A. McPherson (UC Irvine), R. Stevens
(Scripps), G. Schultz (Freiburg), P. Fromme (Arizona State), V. Luzzati
(CNRS), J-m Garcia-Ruiz (Granada), E. Garfield (Chairman emeritus ISI),
A. Khan (TCD), M. Caffrey (Limerick), and author of the book J. D.
Bernal. The Sage of Science, A. Brown.

 

 

Contact, presentation and poster details: [EMAIL PROTECTED] 

 

Website: http://www.bacg.org.uk/

 

[ccp4bb] Post-doctoral position

[Margaret Phillips]

I currently have an open post-doctoral position for a project to crystallize
parasite proteins as part of a drug discovery effort. For anyone interested
in applying please email a copy of your cv and three letters of reference to
the address below.




---
Meg Phillips, Ph.D.
Professor
Dept. of Pharmacology
University of Texas Southwestern Med Center
6001 Forest Park, ND8.120
Dallas, TX   75390-9041
214-645-6164
fax 214-645-6166

email: [EMAIL PROTECTED]

[ccp4bb] crystal shipping at room temperature

[Junhua Pan]

Dear all,

Sorry for the non CCP4 questions. We would like to ship some virus crystals to 
a synchrotron at room temperature (for room temperature diffraction). I am 
wondering if anybody has ever had any good experience for this kind of 
shipping. Especially, it would be great if anybody has any good ideas other 
than pre-mounting the crystals in quartz capillaries (I won't be driving from 
Houston to Chicago though :D). I would also like to know more about the things 
that I need to pay extra attention to, if I have to deal with capillaries. Any 
suggestions would be greatly appreciated.

I'm now testing the more convenient MiTeGen MicroMounts. However, I am not sure 
whether the crystals can remain resting on the MicroMounts aperture during the 
course of a typical Fedex shipping (according to the MicroMounts instruction 
sheet, crystals should not be trapped in the aperture). It would be great if 
anybody would share your previous experience with regard to the MiTeGen stuff. 

Another question about the MiTeGen mounting tools is that I always observe a 
stong diffraction ring at about 5 A. Well, it is not exactly a ring; it's 
actually two thick arches (pretty thick, roughly from 5.5 A to 4.8 A), one at 
the top and the other at the bottom of the diffraction patterns (nothing on the 
left-hand or right-hand side). Does anybody have any idea what this might be 
(fiber?)?

thanks a lot for your help!
 
Junhua  
---
Junhua Pan
Department of Biochemistry & Cell Biology
327 Keck Hall, Rice University
6100 Main Street MS-140
Houston, TX 77005
Phone:  (713)348-3346
Email:  [EMAIL PROTECTED]

Re: [ccp4bb] crystal shipping at room temperature

[William Scott]

Hi Junhua:

These are ccp4 bb questions, so don't apologize (or we all will start
having to do so).

All of my room-temperature shipping experiences are pre 9-11-2001, and
involve carrying stuff with me on airplanes, which is now an impossibility
(unless you possess a Saudi diplomatic pouch, but in that case you
probably can afford your own private jet).

Options like Fed Exp will subject your crystals to large temperature
fluctuations, and probably major blunt trauma injuries.

I would probably either figure out how to freeze them, or drive them from
Houston to Chicago. A third option is to ship the ingredients, and then
grow the crystals there. It might be worth the extra airplane fare.

Bill



Junhua Pan wrote:
> Dear all,
>
> Sorry for the non CCP4 questions. We would like to ship some virus
> crystals to a synchrotron at room temperature (for room temperature
> diffraction). I am wondering if anybody has ever had any good experience
> for this kind of shipping. Especially, it would be great if anybody has
> any good ideas other than pre-mounting the crystals in quartz capillaries
> (I won't be driving from Houston to Chicago though :D). I would also like
> to know more about the things that I need to pay extra attention to, if I
> have to deal with capillaries. Any suggestions would be greatly
> appreciated.
>
> I'm now testing the more convenient MiTeGen MicroMounts. However, I am not
> sure whether the crystals can remain resting on the MicroMounts aperture
> during the course of a typical Fedex shipping (according to the
> MicroMounts instruction sheet, crystals should not be trapped in the
> aperture). It would be great if anybody would share your previous
> experience with regard to the MiTeGen stuff.
>
> Another question about the MiTeGen mounting tools is that I always observe
> a stong diffraction ring at about 5 A. Well, it is not exactly a ring;
> it's actually two thick arches (pretty thick, roughly from 5.5 A to 4.8
> A), one at the top and the other at the bottom of the diffraction patterns
> (nothing on the left-hand or right-hand side). Does anybody have any idea
> what this might be (fiber?)?
>
> thanks a lot for your help!
>
> Junhua
> ---
> Junhua Pan
> Department of Biochemistry & Cell Biology
> 327 Keck Hall, Rice University
> 6100 Main Street MS-140
> Houston, TX 77005
> Phone:  (713)348-3346
> Email:  [EMAIL PROTECTED]
>

Re: [ccp4bb] crystal shipping at room temperature

[Manish C Pathak]

Hi Junhua & Bill,

I wonder about growing crystals in some kind of gel. Long back, i 
received the crystals in gel, and they did diffract. Is it still in 
practice ?

regards
Manish


William Scott <[EMAIL PROTECTED]> wrote: Hi Junhua:

These are ccp4 bb questions, so don't apologize (or we all will start
having to do so).

All of my room-temperature shipping experiences are pre 9-11-2001, and
involve carrying stuff with me on airplanes, which is now an impossibility
(unless you possess a Saudi diplomatic pouch, but in that case you
probably can afford your own private jet).

Options like Fed Exp will subject your crystals to large temperature
fluctuations, and probably major blunt trauma injuries.

I would probably either figure out how to freeze them, or drive them from
Houston to Chicago. A third option is to ship the ingredients, and then
grow the crystals there. It might be worth the extra airplane fare.

Bill



Junhua Pan wrote:
> Dear all,
>
> Sorry for the non CCP4 questions. We would like to ship some virus
> crystals to a synchrotron at room temperature (for room temperature
> diffraction). I am wondering if anybody has ever had any good experience
> for this kind of shipping. Especially, it would be great if anybody has
> any good ideas other than pre-mounting the crystals in quartz capillaries
> (I won't be driving from Houston to Chicago though :D). I would also like
> to know more about the things that I need to pay extra attention to, if I
> have to deal with capillaries. Any suggestions would be greatly
> appreciated.
>
> I'm now testing the more convenient MiTeGen MicroMounts. However, I am not
> sure whether the crystals can remain resting on the MicroMounts aperture
> during the course of a typical Fedex shipping (according to the
> MicroMounts instruction sheet, crystals should not be trapped in the
> aperture). It would be great if anybody would share your previous
> experience with regard to the MiTeGen stuff.
>
> Another question about the MiTeGen mounting tools is that I always observe
> a stong diffraction ring at about 5 A. Well, it is not exactly a ring;
> it's actually two thick arches (pretty thick, roughly from 5.5 A to 4.8
> A), one at the top and the other at the bottom of the diffraction patterns
> (nothing on the left-hand or right-hand side). Does anybody have any idea
> what this might be (fiber?)?
>
> thanks a lot for your help!
>
> Junhua
> ---
> Junhua Pan
> Department of Biochemistry & Cell Biology
> 327 Keck Hall, Rice University
> 6100 Main Street MS-140
> Houston, TX 77005
> Phone:  (713)348-3346
> Email:  [EMAIL PROTECTED]
>


   
-
Ready for the edge of your seat? Check out tonight's top picks on Yahoo! TV. 

[ccp4bb] How to determine ligand binding from diffraction pattern?

[Joe Chen]

Dear all,


Is there a simple way to determine whether ligand is bound or not by
comparing the diffraction patterns between ligand-free (structure known) and
ligand-soaked protein crystals?  I would like to solve the ligand bound
protein structure, but before I do so, I have to find out if the ligand is
actually bound.  Thank you very much!


Best,


Joe

[ccp4bb] A babyish question on coot

[Yanming Zhang]

Hi,

I use coot almost around the clock. One thing troubles me is that:
when clicking on 'real space refine zone', coot seems only care about the 
'real space'(Electron density), sometimes it will bring the model to 
the density no matter whether the density was already  claimed by other 
model atoms or not, resulting in clash and unreasonable geometry. How can 
I avoid this?


Sorry for an old crystallographer to ask so babyish question. But your 
help can save me lots of time.

Thanks
Yanming

Re: [ccp4bb] A babyish question on coot

[Josiah Obiero]

Try alternate rotamers first, and then choose the closest to the 
'right' electron density, before you do 'real space refine'
Regards,
Josiah.

Hi,

I use coot almost around the clock. One thing troubles me is that:
when clicking on 'real space refine zone', coot seems only care about 
the 
'real space'(Electron density), sometimes it will bring the model to 
the density no matter whether the density was already  claimed by other 
model atoms or not, resulting in clash and unreasonable geometry. How 
can 
I avoid this?

Sorry for an old crystallographer to ask so babyish question. But your 
help can save me lots of time.
Thanks
Yanming

Re: [ccp4bb] A babyish question on coot

[Nian Huang]

Optimize zone is also a good choice. Just drag it to the right
conformation. Hold Ctrl to drag only one atom. If you include a region
for real space refinement, there will be no clashes between amino
acids in the region.

Nian

On 5/28/07, Yanming Zhang <[EMAIL PROTECTED]> wrote:

Hi,

I use coot almost around the clock. One thing troubles me is that:
when clicking on 'real space refine zone', coot seems only care about the
'real space'(Electron density), sometimes it will bring the model to
the density no matter whether the density was already  claimed by other
model atoms or not, resulting in clash and unreasonable geometry. How can
I avoid this?

Sorry for an old crystallographer to ask so babyish question. But your
help can save me lots of time.
Thanks
Yanming

Re: [ccp4bb] crystal shipping at room temperature

[Juergen Bosch]

Hi Junhua,

you should contact TSA in Houston, speak to them prior to your flight 
arrange a contact person who will be there when you are traveling. Send 
them a Fax explaining what and why you are carrying your crystals with 
you and how e.g. small cooler with pads etc. I carried some RT 96 well 
trays from Seattle to the Berkeley and Stanford in 2004/2005 without 
troubles. Now things might have changed again with the "3 once liquid 
rule". It might also help if you have an "American" take care of your 
crystals during the flight. People with visa's might be too suspicious.


Main point plan ahead and speak to the authorities. I wouldn't trust 
Fedex with RT crystals. Or drive them yourself to Chicago (2 days ?).


Jürgen


Junhua Pan wrote:


Dear all,

Sorry for the non CCP4 questions. We would like to ship some virus crystals to 
a synchrotron at room temperature (for room temperature diffraction). I am 
wondering if anybody has ever had any good experience for this kind of 
shipping. Especially, it would be great if anybody has any good ideas other 
than pre-mounting the crystals in quartz capillaries (I won't be driving from 
Houston to Chicago though :D). I would also like to know more about the things 
that I need to pay extra attention to, if I have to deal with capillaries. Any 
suggestions would be greatly appreciated.

I'm now testing the more convenient MiTeGen MicroMounts. However, I am not sure whether the crystals can remain resting on the MicroMounts aperture during the course of a typical Fedex shipping (according to the MicroMounts instruction sheet, crystals should not be trapped in the aperture). It would be great if anybody would share your previous experience with regard to the MiTeGen stuff. 


Another question about the MiTeGen mounting tools is that I always observe a 
stong diffraction ring at about 5 A. Well, it is not exactly a ring; it's 
actually two thick arches (pretty thick, roughly from 5.5 A to 4.8 A), one at 
the top and the other at the bottom of the diffraction patterns (nothing on the 
left-hand or right-hand side). Does anybody have any idea what this might be 
(fiber?)?

thanks a lot for your help!

Junhua  
---
Junhua Pan
Department of Biochemistry & Cell Biology
327 Keck Hall, Rice University
6100 Main Street MS-140
Houston, TX 77005
Phone:  (713)348-3346
Email:  [EMAIL PROTECTED]

 




--
Jürgen Bosch
University of Washington
Dept. of Biochemistry, K-426
1705 NE Pacific Street
Seattle, WA 98195
Box 357742
Phone:   +1-206-616-4510
FAX: +1-206-685-7002

Re: [ccp4bb] crystal shipping at room temperature

[Julie Bouckaert]

I know this is not what you ask for, but I have had good experience with 
mounting in capillaries (borosilicate, a bit stronger than quartz, but quartz 
should work also if you are very careful), leaving the crystals in the mother 
liquid, to fly them over by FEDex from USA to Europe. Leave the capillaries at 
the longest length possible, so that someone at the synchrotron can open the 
capillary and push the crystal out of the liquid and close again the capillary, 
or even push the crystal out and remount the crystal in a different way. For 
the flights, I left the cappilaries pending a little loosely in the air, with 
their ends stuck into cotton balls, into a smaller box, that on its turn was 
fixed shock-damping stuff into a strong, uncrushable box. Cheap, quick and 
easy! 

Julie

>Dear all,
>
>Sorry for the non CCP4 questions. We would like to ship some virus crystals to 
>a synchrotron at room temperature (for room temperature diffraction). I am 
>wondering if anybody has ever had any good experience for this kind of 
>shipping. Especially, it would be great if anybody has any good ideas other 
>than pre-mounting the crystals in quartz capillaries (I won't be driving from 
>Houston to Chicago though :D). I would also like to know more about the things 
>that I need to pay extra attention to, if I have to deal with capillaries. Any 
>suggestions would be greatly appreciated.
>
>I'm now testing the more convenient MiTeGen MicroMounts. However, I am not 
>sure whether the crystals can remain resting on the MicroMounts aperture 
>during the course of a typical Fedex shipping (according to the MicroMounts 
>instruction sheet, crystals should not be trapped in the aperture). It would 
>be great if anybody would share your previous experience with regard to the 
>MiTeGen stuff. 
>
>Another question about the MiTeGen mounting tools is that I always observe a 
>stong diffraction ring at about 5 A. Well, it is not exactly a ring; it's 
>actually two thick arches (pretty thick, roughly from 5.5 A to 4.8 A), one at 
>the top and the other at the bottom of the diffraction patterns (nothing on 
>the left-hand or right-hand side). Does anybody have any idea what this might 
>be (fiber?)?
>
>thanks a lot for your help!
> 
>Junhua 
>---
>Junhua Pan
>Department of Biochemistry & Cell Biology
>327 Keck Hall, Rice University
>6100 Main Street MS-140
>Houston, TX 77005
>Phone:  (713)348-3346
>Email:  [EMAIL PROTECTED]
>
>