Re: [ccp4bb] how to overlap DNA

[Nicolas Foos]

Dear Leo,

I use "*superpose*" included in the ccp4 programms suite. You can manage 
a lot of parameters.


In my case for exemple, i use the "superpose specified atoms/residues"

I defined the model which move et the one wich is the reference.

I precise the residues range (in DNA case residue means you base).
And it work very fine.

But your own method depend of what you want to do with your overlaped 
structure.


Hope to help you.

Nicolas






Le 03/05/12 03:18, Junfeng Liu a écrit :

  Dear All,
   Does anybody has the experience to overlap DNA in the  protein
complex? I have tried the LSQ in Coot and it works ok but  not
perfectly. Could you please tell me a better way to do that?Or can
Coot be used to overlap  DNA/RNA on their  back bone  by LSQ or SSM ?
At   the same time, are there some software or servers can be used to
  search the "homology DNA " in the database like the Dali on
protein?
   Thanks in advance!
   Best wishes
   leo

Re: [ccp4bb] how to overlap DNA

[Tim Gruene]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

Dear leo,

how do you mean 'not perfect'? Superposition is not too difficult a
task once you have defined the atoms you want to superpose and there
should not be much variation.

You could fine-tune your result with lsqman (USF program suite) which
allows to specify every single atom pair used in superposition.

Cheers,
Tim

On 05/03/12 03:18, Junfeng Liu wrote:
> Dear All, Does anybody has the experience to overlap DNA in the
> protein complex? I have tried the LSQ in Coot and it works ok but
> not perfectly. Could you please tell me a better way to do that?Or
> can Coot be used to overlap  DNA/RNA on their  back bone  by LSQ or
> SSM ? At   the same time, are there some software or servers can be
> used to search the "homology DNA " in the database like the Dali
> on protein? Thanks in advance! Best wishes leo
> 

- -- 
- --
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen

GPG Key ID = A46BEE1A

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NLAdemJUJDPTyq8AiSdONoA=
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[ccp4bb] Beamline Scientist (I03) position available at DIAMOND

[Katherine McAuley]

Dear all,

Following from Martin's post yesterday, we also have a beamline scientist 
vacancy at Diamond to join the I03 beamline team. I03 provides a facility for 
the determination of biological macromolecules using X-ray diffraction. The 
beamline is equipped with a state of the art experimental end-station which can 
be operated to work with hazard group 3 pathogens.

This vacancy offers an exciting opportunity to be involved in the development 
of the unique infrastructure that I03 will provide to the user community. The 
successful candidate will also be expected to develop an internationally 
competitive research programme in structural biology that complements the 
research and development activities within the MX village.

Full details of the post and how to apply can be found here:
http://www.diamond.ac.uk/Home/Jobs/Current/DIA0731_TH.html

Informal inquires can be directed to Katherine McAuley either by telephone 
(+44(0)1235 778404) or by email: katherine.mcau...@diamond.ac.uk.

The closing date is 31st May 2012 and interviews will be held on 13th June.

Best Regards,

Katherine

[ccp4bb] effective iodide conc. for SAD data

[Rajesh Kumar]

Dear All,
I have very thin crystals but diffracting. I was not able to handle them easily 
for iodide soak. I always lost the crystals during manipulation and other big 
crystals obtained after seeding doesn't even give any diffraction. I tried for 
co-crystallizing with NaI. The crystals appear only up to 20 mM in 1:2 (3ul 
drop of 1 ul protein and 2ul reservoir).Is this concentration of iodide is 
enough for SAD data  ( if it had good incorporation) ?I appreciate your help.
ThanksRajesh  

Re: [ccp4bb] effective iodide conc. for SAD data

[Jan Abendroth]

Hi Rajesh,
it can be a bit all over the place:
For quick soaks, we typically use 500mM-1000mM. A good starting point might be 
to simply replace the NaCl concentration in your protein buffer. By some 
serendipity we also managed to solve a structure by I/S SAD after a 1mM NaI 
soak. One iodide had found its way into a nice binding pocket. 
For co-crystallization, mostly 200mM should be fine.
Another approach could be to supplement your cryo buffer with iodide, replacing 
NaCl. NaI is highly soluble in ethylene glycol.

Also see here: http://www.ncbi.nlm.nih.gov/pubmed/21359836

Good luck!
Cheers,
Jan
--
Jan Abendroth
Emerald Bio
Seattle / Bainbridge Island WA, USA
home: Jan.Abendroth_at_gmail.com
work: JAbendroth_at_embios.com
http://www.emeraldbiostructures.com

On May 3, 2012, at 6:51 AM, Rajesh Kumar wrote:

> Dear All,
> 
> I have very thin crystals but diffracting. I was not able to handle them 
> easily for iodide soak. I always lost the crystals during manipulation and 
> other big crystals obtained after seeding doesn't even give any diffraction. 
> I tried for co-crystallizing with NaI. The crystals appear only up to 20 mM 
> in 1:2 (3ul drop of 1 ul protein and 2ul reservoir).
> Is this concentration of iodide is enough for SAD data  ( if it had good 
> incorporation) ?
> I appreciate your help.
> 
> Thanks
> Rajesh

[ccp4bb] PhD Position at the Institut de Biologie Structurale Jean-Pierre Ebel Grenoble

[Monika Spano]

PhD Position at the Institut de Biologie Structurale Jean-Pierre Ebel Grenoble
A PhD position is available in the Synchrotron Group headed by Dr Jean-Luc 
Ferrer at the Institut de Biologie Structurale (IBS) at Grenoble, starting in 
Autumn 2012. IBS is close to the European large instruments, the ILL and the 
ESRF. The project aims at developing an automated microfluidic pipeline for 
protein crystallization. It combines the control of temperature and precipitant 
concentration in a user-friendly setup allowing for screening in microfluidic 
chips, in situ diffraction screening, and systematic optimization based on the 
phase diagram and finally reliable mounting of crystals for data collection. 
The pipeline consists of three elements: the microchip for screening, the 
optimization platform and robotic crystal mounting.
We are looking for an enthusiastic academically qualified physicist, chemist or 
engineer with a strong interest in structural biology. The candidate should 
have affinity to multi-disciplinary problems. Experience in macromolecular 
crystallization and/or crystallography is welcome. Given the scope of the 
project and the need for a close collaboration with the other team members as 
well as with the industrial/external partners excellent communicative skills 
and the ability to work in a team with biologists and engineers are 
prerequisites.
More information on the PhD position can be obtained from:
Monika Budayova-Spano, PhD
Assistant Professor, Faculty of Pharmacy, University Joseph Fourier
Tel: + 33 4 38 78 96 13
Fax: + 33 4 38 78 51 22
Email: monika.sp...@ibs.fr
For application please supply the following: a detailed resume, a covering 
letter explaining the applicant’s motivation for the position, detailed exam 
results, two references : the name and contact details of at least two people 
who could be contacted to provide an appreciation of the candidat. Please, send 
it to monika.sp...@ibs.fr and to jean-luc.fer...@ibs.fr.

__
Monika Budayova-Spano, PhD
Assistant Professor, Faculty of Pharmacy, University Joseph Fourier
Synchrotron Group
Institut de Biologie Structurale J. P. Ebel
CEA-CNRS-UJF UMR 5075
41, Rue Jules Horowitz
38027 Grenoble cedex 1
Tel: + 33 4 38 78 96 13
Fax: + 33 4 38 78 51 22
Email: monika.sp...@ibs.fr

Re: [ccp4bb] effective iodide conc. for SAD data

[Jim Pflugrath]

Iodide is a fantastic derivative.  One does not need a lot with modern X-ray 
equipment, careful data collection, and great software.


From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Rajesh Kumar 
[ccp4...@hotmail.com]
Sent: Thursday, May 03, 2012 8:51 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] effective iodide conc. for SAD data

Dear All,

I have very thin crystals but diffracting. I was not able to handle them easily 
for iodide soak. I always lost the crystals during manipulation and other big 
crystals obtained after seeding doesn't even give any diffraction. I tried for 
co-crystallizing with NaI. The crystals appear only up to 20 mM in 1:2 (3ul 
drop of 1 ul protein and 2ul reservoir).
Is this concentration of iodide is enough for SAD data  ( if it had good 
incorporation) ?
I appreciate your help.

Thanks
Rajesh

Re: [ccp4bb] effective iodide conc. for SAD data

[Roger Rowlett]

Rajesh,

Why not try a soak-in-place by adding iodide and/or cryoprotectant 
directly to the crystallization drop? Then you only have to fish out the 
crystal once, minimizing handling. I usually do this by preparing an 
artificial mother liquor solution that has 125% of the final desired 
concentration of cryoprotectant and/or ligand. Add 4 volumes of this 
solution to your crystallization drop all at once or in stages. (I 
usually add 0.25, 0.25, 0.5, 1.0, and 2.0 drop volumes a few minutes 
apart). The drop can be incubated over its reservoir well during this 
procedure between additions to minimize evaporation. This often works 
well for fragile crystals or crystals that are sensitive to evaporation 
of the drop.


Cheers,

___
Roger S. Rowlett
Gordon & Dorothy Kline Professor
Department of Chemistry
Colgate University
13 Oak Drive
Hamilton, NY 13346

tel: (315)-228-7245
ofc: (315)-228-7395
fax: (315)-228-7935
email: rrowl...@colgate.edu

On 5/3/2012 9:51 AM, Rajesh Kumar wrote:

Dear All,

I have very thin crystals but diffracting. I was not able to handle 
them easily for iodide soak. I always lost the crystals during 
manipulation and other big crystals obtained after 
seeding doesn't even give any diffraction. I tried for 
co-crystallizing with NaI. The crystals appear only up to 20 mM in 1:2 
(3ul drop of 1 ul protein and 2ul reservoir).
Is this concentration of iodide is enough for SAD data ( if it had 
good incorporation) ?

I appreciate your help.

Thanks
Rajesh

Re: [ccp4bb] effective iodide conc. for SAD data

[Jacob Keller]

I have wondered for a long time now why it is not standard practice for all
crystallization protein stocks to contain either Br- or I- ions instead of
Cl-, even for cationic buffers like TRIS, which could be titrated with HBr
or HI to get in the 10+ mM range. Also, one could use Cs or Rb for the
cations (and titrate anionic buffers with the respective hydroxides).
What's there to lose? The gain is obviously the possible anomalous signal
(always helpful), and one might pick up additional interesting and possibly
physiologically-relevant halide or alkali metal sites. Seems that
structural genomics people might standardize this into the pipeline as
well, and thereby potentially cut out SeMet protein production in many if
not most cases.

JPK

On Thu, May 3, 2012 at 9:05 AM, Jan Abendroth wrote:

> Hi Rajesh,
> it can be a bit all over the place:
> For quick soaks, we typically use 500mM-1000mM. A good starting point
> might be to simply replace the NaCl concentration in your protein buffer.
> By some serendipity we also managed to solve a structure by I/S SAD after a
> 1mM NaI soak. One iodide had found its way into a nice binding pocket.
> For co-crystallization, mostly 200mM should be fine.
> Another approach could be to supplement your cryo buffer with iodide,
> replacing NaCl. NaI is highly soluble in ethylene glycol.
>
> Also see here: http://www.ncbi.nlm.nih.gov/pubmed/21359836
>
> Good luck!
> Cheers,
> Jan
>  --
> Jan Abendroth
> Emerald Bio
> Seattle / Bainbridge Island WA, USA
> home: Jan.Abendroth_at_gmail.com
> work: JAbendroth_at_embios.com
> http://www.emeraldbiostructures.com
>
> On May 3, 2012, at 6:51 AM, Rajesh Kumar wrote:
>
> Dear All,
>
> I have very thin crystals but diffracting. I was not able to handle them
> easily for iodide soak. I always lost the crystals during manipulation
> and other big crystals obtained after seeding doesn't even give any
> diffraction. I tried for co-crystallizing with NaI. The crystals appear
> only up to 20 mM in 1:2 (3ul drop of 1 ul protein and 2ul reservoir).
> Is this concentration of iodide is enough for SAD data  ( if it had good
> incorporation) ?
> I appreciate your help.
>
> Thanks
> Rajesh
>
>
>


-- 
***
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
email: j-kell...@northwestern.edu
***

[ccp4bb] Off Topic: Sucrose / Glycerol Gradient Maker & Fractionator

[Antony Oliver]

Dear all,

I find myself working on a number of  large multi-protein complexes, and am 
likely to need to use Sucrose / Glycerol gradients in preparing them.
IWhilst I can do this manually in the short term,  I was wondering if someone 
could recommend any manufacturer's (preferably Europe/UK based) that make 
suitable systems for:

  1.  Making the gradients in the first place
  2.  Fractionating the gradients after they have been in the centrifuge.

With a great many thanks,

Tony.


---
Dr Antony W Oliver

Senior Research Fellow
CR-UK DNA Repair Enzymes Group
Genome Damage and Stability Centre
Science Park Road
University of Sussex
Falmer, Brighton, BN1 9RQ

email: antony.oli...@sussex.ac.uk
tel (office): +44 (0)1273 678349
tel (lab): +44 (0)1273 677512

Re: [ccp4bb] effective iodide conc. for SAD data

[Roger Rowlett]

Interesting idea. The only caveat that springs to mind is that the more 
useful anions (e.g., iodide and bromide) are on the chaotropic end of 
the Hofmeister series and may potentially destabilize protein structure 
or protein-protein interactions, which might complicate 
co-crystallization starting from known conditions, especially at higher 
concentrations of anion. Alternate cations may be less problematic.


Cheers,

___
Roger S. Rowlett
Gordon & Dorothy Kline Professor
Department of Chemistry
Colgate University
13 Oak Drive
Hamilton, NY 13346

tel: (315)-228-7245
ofc: (315)-228-7395
fax: (315)-228-7935
email: rrowl...@colgate.edu

On 5/3/2012 11:29 AM, Jacob Keller wrote:
I have wondered for a long time now why it is not standard practice 
for all crystallization protein stocks to contain either Br- or I- 
ions instead of Cl-, even for cationic buffers like TRIS, which could 
be titrated with HBr or HI to get in the 10+ mM range. Also, one could 
use Cs or Rb for the cations (and titrate anionic buffers with the 
respective hydroxides). What's there to lose? The gain is obviously 
the possible anomalous signal (always helpful), and one might pick up 
additional interesting and possibly physiologically-relevant halide or 
alkali metal sites. Seems that structural genomics people might 
standardize this into the pipeline as well, and thereby potentially 
cut out SeMet protein production in many if not most cases.


JPK

On Thu, May 3, 2012 at 9:05 AM, Jan Abendroth > wrote:


Hi Rajesh,
it can be a bit all over the place:
For quick soaks, we typically use 500mM-1000mM. A good starting
point might be to simply replace the NaCl concentration in your
protein buffer. By some serendipity we also managed to solve a
structure by I/S SAD after a 1mM NaI soak. One iodide had found
its way into a nice binding pocket.
For co-crystallization, mostly 200mM should be fine.
Another approach could be to supplement your cryo buffer with
iodide, replacing NaCl. NaI is highly soluble in ethylene glycol.

Also see here: http://www.ncbi.nlm.nih.gov/pubmed/21359836

Good luck!
Cheers,
Jan
--
Jan Abendroth
Emerald Bio
Seattle / Bainbridge Island WA, USA
home: Jan.Abendroth_at_gmail.com 
work: JAbendroth_at_embios.com
http://www.emeraldbiostructures.com

On May 3, 2012, at 6:51 AM, Rajesh Kumar wrote:


Dear All,

I have very thin crystals but diffracting. I was not able to
handle them easily for iodide soak. I always lost the crystals
during manipulation and other big crystals obtained after
seeding doesn't even give any diffraction. I tried for
co-crystallizing with NaI. The crystals appear only up to 20 mM
in 1:2 (3ul drop of 1 ul protein and 2ul reservoir).
Is this concentration of iodide is enough for SAD data ( if it
had good incorporation) ?
I appreciate your help.

Thanks
Rajesh





--
***
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
email: j-kell...@northwestern.edu 
***

Re: [ccp4bb] Off Topic: Sucrose / Glycerol Gradient Maker & Fractionator

[Pius Padayatti]

In US Fisher Scientific sells CBS scientific , California different
ranges of gradient maker. I especially found them useful for my use
for density gradient centrifugation. the material
used in the manufacture is clear and easy to clean each time.
It is kind of not very controlled automatically but works well for
membrane preps regularly.

link:http://www.cbsscientific.com/gradientmakers.aspx

The tube puncture using a regular syringe works fantastic.


On Thu, May 3, 2012 at 11:40 AM, Antony Oliver
 wrote:
> Dear all,
>
> I find myself working on a number of  large multi-protein complexes, and am
> likely to need to use Sucrose / Glycerol gradients in preparing them.
> IWhilst I can do this manually in the short term,  I was wondering if
> someone could recommend any manufacturer's (preferably Europe/UK based) that
> make suitable systems for:
>
> Making the gradients in the first place
> Fractionating the gradients after they have been in the centrifuge.
>
> With a great many thanks,
>
> Tony.
>
>
> ---
> Dr Antony W Oliver
>
> Senior Research Fellow
> CR-UK DNA Repair Enzymes Group
> Genome Damage and Stability Centre
> Science Park Road
> University of Sussex
> Falmer, Brighton, BN1 9RQ
>
> email: antony.oli...@sussex.ac.uk
> tel (office): +44 (0)1273 678349
> tel (lab): +44 (0)1273 677512
>



-- 
Pius S Padayatti,PhD,
Phone: 216-658-4528

Re: [ccp4bb] effective iodide conc. for SAD data

[Jim Pflugrath]

Please see my poster at the ACA 2012 meeting.  See also:
(1) Dauter, Z., Dauter, M. & Rajashankar, K.R. (2000) Acta Cryst. D56, 232-237.
(2) Nagem, R.A.P, Dauter, Z. & Polikarpov, I. (2001) Acta Cryst. D57, 996-1002.

:)


From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Roger Rowlett 
[rrowl...@colgate.edu]
Sent: Thursday, May 03, 2012 11:00 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] effective iodide conc. for SAD data

Interesting idea. The only caveat that springs to mind is that the more useful 
anions (e.g., iodide and bromide) are on the chaotropic end of the Hofmeister 
series and may potentially destabilize protein structure or protein-protein 
interactions, which might complicate co-crystallization starting from known 
conditions, especially at higher concentrations of anion. Alternate cations may 
be less problematic.

Cheers,

___
Roger S. Rowlett
Gordon & Dorothy Kline Professor
Department of Chemistry
Colgate University
13 Oak Drive
Hamilton, NY 13346

tel: (315)-228-7245
ofc: (315)-228-7395
fax: (315)-228-7935
email: rrowl...@colgate.edu

On 5/3/2012 11:29 AM, Jacob Keller wrote:
I have wondered for a long time now why it is not standard practice for all 
crystallization protein stocks to contain either Br- or I- ions instead of Cl-, 
even for cationic buffers like TRIS, which could be titrated with HBr or HI to 
get in the 10+ mM range. Also, one could use Cs or Rb for the cations (and 
titrate anionic buffers with the respective hydroxides). What's there to lose? 
The gain is obviously the possible anomalous signal (always helpful), and one 
might pick up additional interesting and possibly physiologically-relevant 
halide or alkali metal sites. Seems that structural genomics people might 
standardize this into the pipeline as well, and thereby potentially cut out 
SeMet protein production in many if not most cases.

JPK

On Thu, May 3, 2012 at 9:05 AM, Jan Abendroth 
mailto:jan.abendr...@gmail.com>> wrote:
Hi Rajesh,
it can be a bit all over the place:
For quick soaks, we typically use 500mM-1000mM. A good starting point might be 
to simply replace the NaCl concentration in your protein buffer. By some 
serendipity we also managed to solve a structure by I/S SAD after a 1mM NaI 
soak. One iodide had found its way into a nice binding pocket.
For co-crystallization, mostly 200mM should be fine.
Another approach could be to supplement your cryo buffer with iodide, replacing 
NaCl. NaI is highly soluble in ethylene glycol.

Also see here: http://www.ncbi.nlm.nih.gov/pubmed/21359836

Good luck!
Cheers,
Jan
--
Jan Abendroth
Emerald Bio
Seattle / Bainbridge Island WA, USA
home: Jan.Abendroth_at_gmail.com
work: JAbendroth_at_embios.com
http://www.emeraldbiostructures.com

On May 3, 2012, at 6:51 AM, Rajesh Kumar wrote:

Dear All,

I have very thin crystals but diffracting. I was not able to handle them easily 
for iodide soak. I always lost the crystals during manipulation and other big 
crystals obtained after seeding doesn't even give any diffraction. I tried for 
co-crystallizing with NaI. The crystals appear only up to 20 mM in 1:2 (3ul 
drop of 1 ul protein and 2ul reservoir).
Is this concentration of iodide is enough for SAD data  ( if it had good 
incorporation) ?
I appreciate your help.

Thanks
Rajesh




--
***
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
email: j-kell...@northwestern.edu
***

Re: [ccp4bb] Off Topic: Sucrose / Glycerol Gradient Maker & Fractionator

[Nian Huang]

Or make it yourself if you got time.
Anal 
Biochem.1994
Sep;221(2):397-400. A
syringe-based gradient former for linear and exponential gradients.
Shearer G 
Jr.


Nian


On Thu, May 3, 2012 at 10:40 AM, Antony Oliver
wrote:

>   Dear all,
>
>  I find myself working on a number of  large multi-protein complexes, and
> am likely to need to use Sucrose / Glycerol gradients in preparing them.
> IWhilst I can do this manually in the short term,  I was wondering if
> someone could recommend any manufacturer's (preferably Europe/UK based)
> that make suitable systems for:
>
>1. Making the gradients in the first place
>2. Fractionating the gradients after they have been in the centrifuge.
>
> With a great many thanks,
>
>  Tony.
>
>
>   ---
>  Dr Antony W Oliver
>
>  Senior Research Fellow
>  CR-UK DNA Repair Enzymes Group
>  Genome Damage and Stability Centre
>  Science Park Road
>  University of Sussex
>  Falmer, Brighton, BN1 9RQ
>
>  email: antony.oli...@sussex.ac.uk
>  tel (office): +44 (0)1273 678349
>  tel (lab): +44 (0)1273 677512
>
>

Re: [ccp4bb] effective iodide conc. for SAD data

[Florian Sauer]

Dear Rajesh,

another method to incorporate Iodine into your crystal is by simply
placing a drop of KI/I2 solution next to the crystallization drop.

Have a look here:

Acta Cryst. (2006). D62, 280-289
New methods to prepare iodinated derivatives by vaporizing iodine
labelling (VIL) and hydrogen peroxide VIL (HYPER-VIL)

Worked for me with salt concentration sensitive crystal and a
derivatization time <10 min.

Good luck,

Florian




Am 03.05.12 15:51, schrieb Rajesh Kumar:
> Dear All,
>
> I have very thin crystals but diffracting. I was not able to handle
> them easily for iodide soak. I always lost the crystals during
> manipulation and other big crystals obtained after
> seeding doesn't even give any diffraction. I tried for
> co-crystallizing with NaI. The crystals appear only up to 20 mM in 1:2
> (3ul drop of 1 ul protein and 2ul reservoir).
> Is this concentration of iodide is enough for SAD data  ( if it had
> good incorporation) ?
> I appreciate your help.
>
> Thanks
> Rajesh

Re: [ccp4bb] effective iodide conc. for SAD data

[Edward A. Berry]

Did you locate the Iodine(s)? Did you have iodotyrosine, or I^- bound
at anion binding sites? There are two distinct methods based on I2/I-.

Florian Sauer wrote:

  Dear Rajesh,

another method to incorporate Iodine into your crystal is by simply
placing a drop of KI/I2 solution next to the crystallization drop.

Have a look here:

Acta Cryst. (2006). D62, 280-289
New methods to prepare iodinated derivatives by vaporizing iodine
labelling (VIL) and hydrogen peroxide VIL (HYPER-VIL)

Worked for me with salt concentration sensitive crystal and a
derivatization time <10 min.

Good luck,

Florian




Am 03.05.12 15:51, schrieb Rajesh Kumar:

Dear All,

I have very thin crystals but diffracting. I was not able to handle
them easily for iodide soak. I always lost the crystals during
manipulation and other big crystals obtained after seeding doesn't
even give any diffraction. I tried for co-crystallizing with NaI. The
crystals appear only up to 20 mM in 1:2 (3ul drop of 1 ul protein and
2ul reservoir).
Is this concentration of iodide is enough for SAD data ( if it had
good incorporation) ?
I appreciate your help.

Thanks
Rajesh

Re: [ccp4bb] effective iodide conc. for SAD data

[Florian Sauer]

Yes I did and could solve the structure by SAD.

In total 8 I atoms found. 6 bound at anion binding sites. 2 as I2.
None covalently bound to tyrosine.


Florian

Am 03.05.12 19:42, schrieb Edward A. Berry:
> Did you locate the Iodine(s)? Did you have iodotyrosine, or I^- bound
> at anion binding sites? There are two distinct methods based on I2/I-.
>
> Florian Sauer wrote:
>> Dear Rajesh,
>>
>> another method to incorporate Iodine into your crystal is by simply
>> placing a drop of KI/I2 solution next to the crystallization drop.
>>
>> Have a look here:
>>
>> Acta Cryst. (2006). D62, 280-289
>> New methods to prepare iodinated derivatives by vaporizing iodine
>> labelling (VIL) and hydrogen peroxide VIL (HYPER-VIL)
>>
>> Worked for me with salt concentration sensitive crystal and a
>> derivatization time <10 min.
>>
>> Good luck,
>>
>> Florian
>>
>>
>>
>>
>> Am 03.05.12 15:51, schrieb Rajesh Kumar:
>>> Dear All,
>>>
>>> I have very thin crystals but diffracting. I was not able to handle
>>> them easily for iodide soak. I always lost the crystals during
>>> manipulation and other big crystals obtained after seeding doesn't
>>> even give any diffraction. I tried for co-crystallizing with NaI. The
>>> crystals appear only up to 20 mM in 1:2 (3ul drop of 1 ul protein and
>>> 2ul reservoir).
>>> Is this concentration of iodide is enough for SAD data ( if it had
>>> good incorporation) ?
>>> I appreciate your help.
>>>
>>> Thanks
>>> Rajesh
>>
>

[ccp4bb] new fragment library

[Vicki Nienaber]

Hi -Sorry for the slight off-topic.

Passing along that we have a new fragment library - called library 2 (the other 
was library 1).  Same format, dry films in 96 well plates.  The library 
includes additional more specialized cores which we think nicely complement 
library 1.
Some have also asked that we take credit cards and we do now through our online 
store. http://shop.zenobiatherapeutics.com/

You still have to contact us for academic pricing. 
er...@zenobiatherapeutics.com but you 
will be able to use credit cards for that as well.

Also for those of you who used library 1, if you have specific feedback (good 
or bad) please contact Erika.  We've heard good things from crystallographers 
but want to keep improving things.

Thanks
Vicki

Vicki Nienaber, Ph.D.
www.zenobiatherapeutics.com

Re: [ccp4bb] How to overlap DNA

[Junfeng Liu]

Dear Guys,
Thank you very much for your suggestions!
I have tried Superpose from CCP4i as suggested by Arka& Nicolas. It
works fine and can overlap the whole base as the LSQ in coot. The USF
(lsqman suggested by Tim)has not been installed in my PC and I will
try it and see after it has been installed. Any other suggestions are
welcome.
Best wishes
leo

Re: [ccp4bb] effective iodide conc. for SAD data

[Rajesh Kumar]

Dear All,

I really thank everyone who gave me excellent suggestions.
I will try them to see which one works better for me and my crystals.
Again thanks a lot for your help.

Regards,
Rajesh

Date: Thu, 3 May 2012 20:56:21 +0200
From: florian.sa...@embl-hamburg.de
Subject: Re: [ccp4bb] effective iodide conc. for SAD data
To: CCP4BB@JISCMAIL.AC.UK


  

  
  
Yes I did and could solve the structure by SAD.



In total 8 I atoms found. 6 bound at anion binding sites. 2 as I2.

None covalently bound to tyrosine.





Florian



Am 03.05.12 19:42, schrieb Edward A. Berry:

> Did you locate the Iodine(s)?
  Did you have iodotyrosine, or I^- bound

  > at anion binding sites? There are two distinct methods based
  on I2/I-.

  >

  > Florian Sauer wrote:

  >> Dear Rajesh,

  >>

  >> another method to incorporate Iodine into your crystal is
  by simply

  >> placing a drop of KI/I2 solution next to the
  crystallization drop.

  >>

  >> Have a look here:

  >>

  >> Acta Cryst. (2006). D62, 280-289

  >> New methods to prepare iodinated derivatives by
  vaporizing iodine

  >> labelling (VIL) and hydrogen peroxide VIL (HYPER-VIL)

  >>

  >> Worked for me with salt concentration sensitive crystal
  and a

  >> derivatization time <10 min.

  >>

  >> Good luck,

  >>

  >> Florian

  >>

  >>

  >>

  >>

  >> Am 03.05.12 15:51, schrieb Rajesh Kumar:

  >>> Dear All,

  >>>

  >>> I have very thin crystals but diffracting. I was not
  able to handle

  >>> them easily for iodide soak. I always lost the
  crystals during

  >>> manipulation and other big crystals obtained after
  seeding doesn't

  >>> even give any diffraction. I tried for
  co-crystallizing with NaI. The

  >>> crystals appear only up to 20 mM in 1:2 (3ul drop of
  1 ul protein and

  >>> 2ul reservoir).

  >>> Is this concentration of iodide is enough for SAD
  data ( if it had

  >>> good incorporation) ?

  >>> I appreciate your help.

  >>>

  >>> Thanks

  >>> Rajesh

  >>

  >