Re: [ccp4bb] Literature on crystallization screen ingredients not showing up in crystal structure

2018-09-11 Thread Diana Tomchick 
Not being in a model does not show that it's really not there.

This is especially true when considering crystals that diffract to rather low 
resolution (~2.8 - 3.5+ Å).

You shouldn’t expect in that case to uniquely identify very many buffer 
components.

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 Sep 11, 2018, at 7:14 AM, Robbie Joosten 
mailto:robbie_joos...@hotmail.com>> wrote:

Hi Tobias,

I don't know of any specific claims made about this but you'd better check the 
data yourself if you find an example. A nice paper by Bill Hunter and his team 
(http://scripts.iucr.org/cgi-bin/paper?S1744309111005835) showed a case where 
Co2+ was an essential ion for crystallisation , but it was overlooked by the 
original depositors of the model. Not being in a model does not show that it's 
really not there.

Cheers,
Robbie

-Original Message-
From: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK>> 
On Behalf Of Tobias
Beck
Sent: Tuesday, September 11, 2018 13:42
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Literature on crystallization screen ingredients not
showing up in crystal structure

Thanks for the replies I have received so far (on and off list).

I would like to emphasize an important aspect: What about crystallization
trials where the ingredients do not show up, but cannot be omitted for the
crystallization, e.g. buffers to control pH, as mentioned in one response - I
am also thinking of specific ions, that are required, but are disordered - any
general reference for this?


Can't you just point out that crystallization is a purification method
Yes, that would be one way to put it.

Thanks, Tobias.



On Tue, Sep 11, 2018 at 12:38 PM Patrick Shaw Stewart
mailto:patr...@douglas.co.uk> 
 > wrote:



Can't you just point out that crystallization is a purification method?
E.g. look at the number of proteins in the Sigma catalogue that have been
purified by crystallization.  Clearly crystallization often excludes other 
solutes
in the mix.

Best wishes, Patrick


On Tue, 11 Sep 2018 at 08:41, Tobias Beck 
mailto:tobiasb...@gmail.com>
 > wrote:


Dear all,

I am looking for some general references regarding the fact
that for a crystallization condition not all ingredients of the crystallization
cocktail will show up in the crystal structure. Ions could be disordered,
buffer components located in the solvent regions, etc.


I think this is rather common knowledge, but maybe there is,
especially regarding protein crystallization, a more general reference (apart
from text books on solubility) for this and I am just not using the right search
terms...


Thank you!

Best, Tobias.

--

___

Dr. Tobias Beck
- independent group leader -
RWTH Aachen University
Institute of Inorganic Chemistry
Landoltweg 1, office: 304N
52056 Aachen, Germany
phone:  +49-241-80-90057
fax:   +49-241-80-99003
web:  http://www.ac.rwth-aachen.de/extern/beck/
___






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--

 patr...@douglas.co.uk 
 Douglas
Instruments Ltd.
 Douglas House, East Garston, Hungerford, Berkshire, RG17 7HD, UK
 Directors: Peter Baldock, Patrick Shaw Stewart

 http://www.douglas.co.uk
 Tel: 44 (0) 148-864-9090US toll-free 1-877-225-2034
 Regd. England 2177994, VAT Reg. GB 480 7371 36






--

___

Dr. Tobias Beck
- independent group leader -
RWTH Aachen University
Institute of Inorganic Chemistry
Landoltweg 1, office: 304N
52056 Aachen, Germany
phone:  +49-241-80-90057
fax:   +49-241-80-99003
web:  http://www.ac.rwth-aachen.de/extern/beck/
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Re: [ccp4bb] Literature on crystallization screen ingredients not showing up in crystal structure

2018-09-11 Thread Robbie Joosten 
Hi Tobias,

I don't know of any specific claims made about this but you'd better check the 
data yourself if you find an example. A nice paper by Bill Hunter and his team 
(http://scripts.iucr.org/cgi-bin/paper?S1744309111005835) showed a case where 
Co2+ was an essential ion for crystallisation , but it was overlooked by the 
original depositors of the model. Not being in a model does not show that it's 
really not there. 

Cheers,
Robbie

> -Original Message-
> From: CCP4 bulletin board  On Behalf Of Tobias
> Beck
> Sent: Tuesday, September 11, 2018 13:42
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] Literature on crystallization screen ingredients not
> showing up in crystal structure
> 
> Thanks for the replies I have received so far (on and off list).
> 
> I would like to emphasize an important aspect: What about crystallization
> trials where the ingredients do not show up, but cannot be omitted for the
> crystallization, e.g. buffers to control pH, as mentioned in one response - I
> am also thinking of specific ions, that are required, but are disordered - any
> general reference for this?
> 
> 
> > Can't you just point out that crystallization is a purification method
> Yes, that would be one way to put it.
> 
> Thanks, Tobias.
> 
> 
> 
> On Tue, Sep 11, 2018 at 12:38 PM Patrick Shaw Stewart
> mailto:patr...@douglas.co.uk> > wrote:
> 
> 
> 
>   Can't you just point out that crystallization is a purification method?
> E.g. look at the number of proteins in the Sigma catalogue that have been
> purified by crystallization.  Clearly crystallization often excludes other 
> solutes
> in the mix.
> 
>   Best wishes, Patrick
> 
> 
>   On Tue, 11 Sep 2018 at 08:41, Tobias Beck   > wrote:
> 
> 
>   Dear all,
> 
>   I am looking for some general references regarding the fact
> that for a crystallization condition not all ingredients of the 
> crystallization
> cocktail will show up in the crystal structure. Ions could be disordered,
> buffer components located in the solvent regions, etc.
> 
> 
>   I think this is rather common knowledge, but maybe there is,
> especially regarding protein crystallization, a more general reference (apart
> from text books on solubility) for this and I am just not using the right 
> search
> terms...
> 
> 
>   Thank you!
> 
>   Best, Tobias.
> 
>   --
> 
>   ___
> 
>   Dr. Tobias Beck
>   - independent group leader -
>   RWTH Aachen University
>   Institute of Inorganic Chemistry
>   Landoltweg 1, office: 304N
>   52056 Aachen, Germany
>   phone:  +49-241-80-90057
>   fax:   +49-241-80-99003
>   web:  http://www.ac.rwth-aachen.de/extern/beck/
>   ___
> 
> 
> 
> 
> 
> 
>   To unsubscribe from the CCP4BB list, click the following link:
>   https://www.jiscmail.ac.uk/cgi-
> bin/webadmin?SUBED1=CCP4BB=1
> 
> 
> 
>   --
> 
>patr...@douglas.co.uk  Douglas
> Instruments Ltd.
>Douglas House, East Garston, Hungerford, Berkshire, RG17 7HD, UK
>Directors: Peter Baldock, Patrick Shaw Stewart
> 
>http://www.douglas.co.uk
>Tel: 44 (0) 148-864-9090US toll-free 1-877-225-2034
>Regd. England 2177994, VAT Reg. GB 480 7371 36
> 
> 
>  XrN7sKj6v5KRN6W56jV385v7rnbW4WDX_q2HNFv8f197v5Y04?si=7
> 1398361=d783306d-9ddd-4cae-fcf9-ebed897fee90=null>
> 
> 
> 
> --
> 
> ___
> 
> Dr. Tobias Beck
> - independent group leader -
> RWTH Aachen University
> Institute of Inorganic Chemistry
> Landoltweg 1, office: 304N
> 52056 Aachen, Germany
> phone:  +49-241-80-90057
> fax:   +49-241-80-99003
> web:  http://www.ac.rwth-aachen.de/extern/beck/
> ___
> 
> 
> 
> 
> 
> 
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Re: [ccp4bb] Literature on crystallization screen ingredients not showing up in crystal structure

2018-09-11 Thread Christian Roth 
Not quite what you were looking for, but there was just that paper from
Alexander McPherson abut dye binding. They show that some of the dyes seem
to bind really tight to the protein, but are invisible in the structure.
Maybe there are also some interesting references in there. Sorry haven't
got around to read through it by myself, except for the abstract so far.
Cheers
Christian

Investigation into the binding of dyes within protein crystals.


*McPherson A*, Larson SB.

Acta Crystallogr F Struct Biol Commun. 2018 Sep 1;74(Pt 9):593-602. doi:
10.1107/S2053230X18010300. Epub 2018 Sep 3.
PMID:30198893


On Tue, Sep 11, 2018 at 1:42 PM Tobias Beck  wrote:

> Thanks for the replies I have received so far (on and off list).
>
> I would like to emphasize an important aspect: What about crystallization
> trials where the ingredients do not show up, but cannot be omitted for the
> crystallization, e.g. buffers to control pH, as mentioned in one response -
> I am also thinking of specific ions, that are required, but are disordered
> - any general reference for this?
>
> > Can't you just point out that crystallization is a purification method
> Yes, that would be one way to put it.
>
> Thanks, Tobias.
>
>
> On Tue, Sep 11, 2018 at 12:38 PM Patrick Shaw Stewart <
> patr...@douglas.co.uk> wrote:
>
>>
>> Can't you just point out that crystallization is a purification method?
>> E.g. look at the number of proteins in the Sigma catalogue that have been
>> purified by crystallization.  Clearly crystallization often excludes other
>> solutes in the mix.
>>
>> Best wishes, Patrick
>>
>>
>> On Tue, 11 Sep 2018 at 08:41, Tobias Beck  wrote:
>>
>>> Dear all,
>>>
>>> I am looking for some general references regarding the fact that for a
>>> crystallization condition not all ingredients of the crystallization
>>> cocktail will show up in the crystal structure. Ions could be disordered,
>>> buffer components located in the solvent regions, etc.
>>>
>>> I think this is rather common knowledge, but maybe there is, especially
>>> regarding protein crystallization, a more general reference (apart from
>>> text books on solubility) for this and I am just not using the right search
>>> terms...
>>>
>>> Thank you!
>>>
>>> Best, Tobias.
>>> --
>>> ___
>>>
>>> Dr. Tobias Beck
>>> - independent group leader -
>>> RWTH Aachen University
>>> Institute of Inorganic Chemistry
>>> Landoltweg 1, office: 304N
>>> 52056 Aachen, Germany
>>> phone:  +49-241-80-90057
>>> fax:   +49-241-80-99003
>>> web:  http://www.ac.rwth-aachen.de/extern/beck/
>>> ___
>>>
>>>
>>> --
>>>
>>> To unsubscribe from the CCP4BB list, click the following link:
>>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>>>
>>
>>
>> --
>>  patr...@douglas.co.ukDouglas Instruments Ltd.
>>  Douglas House, East Garston, Hungerford, Berkshire, RG17 7HD, UK
>>  Directors: Peter Baldock, Patrick Shaw Stewart
>>
>>  http://www.douglas.co.uk
>>  Tel: 44 (0) 148-864-9090US toll-free 1-877-225-2034
>>  Regd. England 2177994, VAT Reg. GB 480 7371 36
>>
>
>
> --
> ___
>
> Dr. Tobias Beck
> - independent group leader -
> RWTH Aachen University
> Institute of Inorganic Chemistry
> Landoltweg 1, office: 304N
> 52056 Aachen, Germany
> phone:  +49-241-80-90057
> fax:   +49-241-80-99003
> web:  http://www.ac.rwth-aachen.de/extern/beck/
> ___
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>



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Re: [ccp4bb] Literature on crystallization screen ingredients not showing up in crystal structure

2018-09-11 Thread Tobias Beck 
Thanks for the replies I have received so far (on and off list).

I would like to emphasize an important aspect: What about crystallization
trials where the ingredients do not show up, but cannot be omitted for the
crystallization, e.g. buffers to control pH, as mentioned in one response -
I am also thinking of specific ions, that are required, but are disordered
- any general reference for this?

> Can't you just point out that crystallization is a purification method
Yes, that would be one way to put it.

Thanks, Tobias.


On Tue, Sep 11, 2018 at 12:38 PM Patrick Shaw Stewart 
wrote:

>
> Can't you just point out that crystallization is a purification method?
> E.g. look at the number of proteins in the Sigma catalogue that have been
> purified by crystallization.  Clearly crystallization often excludes other
> solutes in the mix.
>
> Best wishes, Patrick
>
>
> On Tue, 11 Sep 2018 at 08:41, Tobias Beck  wrote:
>
>> Dear all,
>>
>> I am looking for some general references regarding the fact that for a
>> crystallization condition not all ingredients of the crystallization
>> cocktail will show up in the crystal structure. Ions could be disordered,
>> buffer components located in the solvent regions, etc.
>>
>> I think this is rather common knowledge, but maybe there is, especially
>> regarding protein crystallization, a more general reference (apart from
>> text books on solubility) for this and I am just not using the right search
>> terms...
>>
>> Thank you!
>>
>> Best, Tobias.
>> --
>> ___
>>
>> Dr. Tobias Beck
>> - independent group leader -
>> RWTH Aachen University
>> Institute of Inorganic Chemistry
>> Landoltweg 1, office: 304N
>> 52056 Aachen, Germany
>> phone:  +49-241-80-90057
>> fax:   +49-241-80-99003
>> web:  http://www.ac.rwth-aachen.de/extern/beck/
>> ___
>>
>>
>> --
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>>
>
>
> --
>  patr...@douglas.co.ukDouglas Instruments Ltd.
>  Douglas House, East Garston, Hungerford, Berkshire, RG17 7HD, UK
>  Directors: Peter Baldock, Patrick Shaw Stewart
>
>  http://www.douglas.co.uk
>  Tel: 44 (0) 148-864-9090US toll-free 1-877-225-2034
>  Regd. England 2177994, VAT Reg. GB 480 7371 36
>


-- 
___

Dr. Tobias Beck
- independent group leader -
RWTH Aachen University
Institute of Inorganic Chemistry
Landoltweg 1, office: 304N
52056 Aachen, Germany
phone:  +49-241-80-90057
fax:   +49-241-80-99003
web:  http://www.ac.rwth-aachen.de/extern/beck/
___



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[ccp4bb] Literature on crystallization screen ingredients not showing up in crystal structure

2018-09-11 Thread Tobias Beck 
Dear all,

I am looking for some general references regarding the fact that for a
crystallization condition not all ingredients of the crystallization
cocktail will show up in the crystal structure. Ions could be disordered,
buffer components located in the solvent regions, etc.

I think this is rather common knowledge, but maybe there is, especially
regarding protein crystallization, a more general reference (apart from
text books on solubility) for this and I am just not using the right search
terms...

Thank you!

Best, Tobias.
-- 
___

Dr. Tobias Beck
- independent group leader -
RWTH Aachen University
Institute of Inorganic Chemistry
Landoltweg 1, office: 304N
52056 Aachen, Germany
phone:  +49-241-80-90057
fax:   +49-241-80-99003
web:  http://www.ac.rwth-aachen.de/extern/beck/
___



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