Re: [ccp4bb] (EXTERNAL) RE: [ccp4bb] Confused about centric reflections

[Edward A. Berry]

On 03/02/2019 09:59 PM, Ronald E. Stenkamp wrote:

I was taught about centric reflections using different words from those in the 
wiki.

If you look at your crystal structure in projection and the planar view looks 
centrosymmetric, the zone of reflections corresponding to that projection will 
have centric phases, i.e., their phases will be restricted to one of two 
values.  Sometimes those phases are restricted to 0 and 180 degrees, other 
times, depending on the location of the pseudo-inversion center, the phases 
might be 90 or 270 degrees.

So if you look down the two-fold axis in P2, the coordinates of equivalent 
positions become x,0,z and (-x,0,-z).  The zone perpendicular to the two-fold 
contains the h0l reflections, and they end up with restricted phases.  For 
orthorhombic structures, all three zones (h0l, hk0, 0kl) are centric.  And if 
you look at trigonal structures, as in P3(1), there are no centric reflections. 
 (In P3(1)21, there are centric zones, but they aren't the hk0 reflections.

Ron Stenkamp


Thanks, I think I see that. Any time you have a two-fold axis, proper or screw, the 
projection of density onto a plane perpendicular to that axis and passing through the 
origin will be 2-fold symmetric. Any reflection whose scattering vector lies within that 
plane will be taken to its Friedel mate by the reciprocal space version of the operator, 
and that reflection's scattering vector will lie along the same line but in the opposite 
direction. The further projection of the density onto one of those scattering vectors 
will obey the 2-fold and be centrosymetric. Centrosymmetry in one-dimension is also 
called "even function" (vs odd function). The fourier components of even 
functions are non-zero only for the cos terms (sin is an odd function), taking zero at 
the point of centrosymmetry. If the center of symmetry is offset from the origin then 
there is a phase shift equal to 2pi times the fractional distance from origin to center 
along the scattering vector. If we don't like negative am
p
litudes, we make them positive and add pi to the phase. So we get 2 possible 
phases, separated by 180*. (Or something like that.)



-Original Message-
From: CCP4 bulletin board  On Behalf Of Edward A. Berry
Sent: Saturday, March 2, 2019 2:00 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Confused about centric reflections

The wiki:

https://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Centric_and_acentric_reflections

says:
"A reflection is centric if there is a reciprocal space symmetry operator which 
maps it onto itself (or rather its Friedel mate).
. . .
Centric reflections in space group P2 and P21 are thus those with 0,k,0."

The operator -h,k,-l does NOT take 0,k,0 to its Friedel mate.
it takes h,0,k to their Friedel mates. In other words the plane perpendicular 
to the 2-fold axis, at 0 along the axis

Or am I missing something?
eab



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Re: [ccp4bb] KCl in SDS-PAGE workarounds?

[Bonsor, Daniel]

SDS is soluble, whereas the potassium salt of dodecyl sulphate is insoluble. 
You could try 18-Crown-6 ether to chelate the potassium, though I don't know if 
the crown ether would then affect the gel.


Dan


Daniel A. Bonsor PhD
Institute of Human Virology,
University of Maryland at Baltimore
725 W. Lombard Street N571
Baltimore
MD 21201



From: CCP4 bulletin board  on behalf of Keller, Jacob 

Sent: Saturday, March 2, 2019 9:52 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] KCl in SDS-PAGE workarounds?


Dear crystallographers,



It has been my experience that KCl does nasty things when loading SDS-PAGE 
gels. Does anyone have an easy workaround, perhaps TCA precipitation? Ideally 
this would be something nicely quantitative yet quick and easy….



Any suggestions appreciated.



All the best,



Jacob Keller



+

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

+



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From: CCP4 bulletin board  On Behalf Of Artem Evdokimov
Sent: Saturday, March 2, 2019 8:32 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] ionic strength for extraction buffer of membrane proteins



Hi Alex,



In my experience you just have to experiment with these parameters (in however 
of a limited space that is afforded by your experimental set-up). If you have 
the right tools you can slog through semifactorial or DoE-based scouting of 
various parameters with relative ease. These parameters typically include pH, 
salinity, detergent(s), and other variables (e.g. the nature of the buffer and 
salt(s) - many cases exist where the 'standard' choices do not work well).



Literature-based analogies do help on occasion. For example, membrane-spanning 
p450-type proteins often prefer high salt, and often would do better in sodium 
acetate as opposed to chloride. I've worked with ion channels that preferred 3M 
NaCl, or 2M MgCl2 and other fairly weird conditions...



Artem

- Cosmic Cats approve of this message





On Fri, Mar 1, 2019 at 7:27 AM Alex Perálvarez Marín 
mailto:aperalva...@gmail.com>> wrote:

Dear all,

any reference as a guide for selecting the appropriate salt and
concentration for membrane proteins extraction buffer?

Best,

Alex

--
Alex Perálvarez-Marín, Ph.D.
Centre d'Estudis en Biofísica / Unitat de Biofísica
Edifici M
Universitat Autònoma de Barcelona
08193 Cerdanyola del Vallés
Barcelona
Spain
Phone: +34 93 581 4504
FAX:  +34 93 581 1907
e-mail: aperalva...@gmail.com
LinkedIn: 
es.linkedin.com/in/aperalvarez/



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[ccp4bb] KCl in SDS-PAGE workarounds?

[Keller, Jacob]

Dear crystallographers,

It has been my experience that KCl does nasty things when loading SDS-PAGE 
gels. Does anyone have an easy workaround, perhaps TCA precipitation? Ideally 
this would be something nicely quantitative yet quick and easy….

Any suggestions appreciated.

All the best,

Jacob Keller

+
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  On Behalf Of Artem Evdokimov
Sent: Saturday, March 2, 2019 8:32 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] ionic strength for extraction buffer of membrane proteins

Hi Alex,

In my experience you just have to experiment with these parameters (in however 
of a limited space that is afforded by your experimental set-up). If you have 
the right tools you can slog through semifactorial or DoE-based scouting of 
various parameters with relative ease. These parameters typically include pH, 
salinity, detergent(s), and other variables (e.g. the nature of the buffer and 
salt(s) - many cases exist where the 'standard' choices do not work well).

Literature-based analogies do help on occasion. For example, membrane-spanning 
p450-type proteins often prefer high salt, and often would do better in sodium 
acetate as opposed to chloride. I've worked with ion channels that preferred 3M 
NaCl, or 2M MgCl2 and other fairly weird conditions...

Artem
- Cosmic Cats approve of this message


On Fri, Mar 1, 2019 at 7:27 AM Alex Perálvarez Marín 
mailto:aperalva...@gmail.com>> wrote:
Dear all,

any reference as a guide for selecting the appropriate salt and
concentration for membrane proteins extraction buffer?

Best,

Alex

--
Alex Perálvarez-Marín, Ph.D.
Centre d'Estudis en Biofísica / Unitat de Biofísica
Edifici M
Universitat Autònoma de Barcelona
08193 Cerdanyola del Vallés
Barcelona
Spain
Phone: +34 93 581 4504
FAX:  +34 93 581 1907
e-mail: aperalva...@gmail.com
LinkedIn: 
es.linkedin.com/in/aperalvarez/



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Re: [ccp4bb] ionic strength for extraction buffer of membrane proteins

[Artem Evdokimov]

Hi Alex,

In my experience you just have to experiment with these parameters (in
however of a limited space that is afforded by your experimental set-up).
If you have the right tools you can slog through semifactorial or DoE-based
scouting of various parameters with relative ease. These parameters
typically include pH, salinity, detergent(s), and other variables (e.g. the
nature of the buffer and salt(s) - many cases exist where the 'standard'
choices do not work well).

Literature-based analogies do help on occasion. For example,
membrane-spanning p450-type proteins often prefer high salt, and often
would do better in sodium acetate as opposed to chloride. I've worked with
ion channels that preferred 3M NaCl, or 2M MgCl2 and other fairly weird
conditions...

Artem
- Cosmic Cats approve of this message


On Fri, Mar 1, 2019 at 7:27 AM Alex Perálvarez Marín 
wrote:

> Dear all,
>
> any reference as a guide for selecting the appropriate salt and
> concentration for membrane proteins extraction buffer?
>
> Best,
>
> Alex
>
> --
> Alex Perálvarez-Marín, Ph.D.
> Centre d'Estudis en Biofísica / Unitat de Biofísica
> Edifici M
> Universitat Autònoma de Barcelona
> 08193 Cerdanyola del Vallés
> Barcelona
> Spain
> Phone: +34 93 581 4504
> FAX:  +34 93 581 1907
> e-mail: aperalva...@gmail.com
> LinkedIn: es.linkedin.com/in/aperalvarez/
>
> 
>
> 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] Confused about centric reflections

[Edward A. Berry]

Thaks! typo- h,0,l not h,0,k
I have not registered for editing on that wiki,
so I was hoping someone else would take care of it.
But it seems all that's needed is to confirm your account, so I'll register and 
give it a try. Hope I don't make things worse!
(what is this urldefense.proofpoint? did my institution add that, or JISCMAIL?)


On 03/02/2019 05:28 PM, Dale Tronrud wrote:

You are correct, other than your typo.  The centric zone in a
monoclinic space group (B setting) is h0l.

This web site is a wiki so you should be able to correct it yourself.

Dale Tronrud

On 3/2/2019 2:00 PM, Edward A. Berry wrote:

The wiki:

https://urldefense.proofpoint.com/v2/url?u=https-3A__strucbio.biologie.uni-2Dkonstanz.de_ccp4wiki_index.php_Centric-5Fand-5Facentric-5Freflections=DwICaQ=ogn2iPkgF7TkVSicOVBfKg=cFgyH4s-peZ6Pfyh0zB379rxK2XG5oHu7VblrALfYPA=HENAQrgItEIhnnUZhWe8GMKW5sRX2v7V-rsby0AB7LQ=8D9Gvr-8AQeITEdUbf2xeIBDNzdTzUTnE78AI70O1J0=


says:
"A reflection is centric if there is a reciprocal space symmetry
operator which maps it onto itself (or rather its Friedel mate).
. . .
Centric reflections in space group P2 and P21 are thus those with 0,k,0."

The operator -h,k,-l does NOT take 0,k,0 to its Friedel mate.
it takes h,0,k to their Friedel mates. In other words the plane
perpendicular to the 2-fold axis, at 0 along the axis

Or am I missing something?
eab



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Re: [ccp4bb] Confused about centric reflections

[Dale Tronrud]

   You are correct, other than your typo.  The centric zone in a
monoclinic space group (B setting) is h0l.

   This web site is a wiki so you should be able to correct it yourself.

Dale Tronrud

On 3/2/2019 2:00 PM, Edward A. Berry wrote:
> The wiki:
> 
> https://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Centric_and_acentric_reflections
> 
> 
> says:
> "A reflection is centric if there is a reciprocal space symmetry
> operator which maps it onto itself (or rather its Friedel mate).
> . . .
> Centric reflections in space group P2 and P21 are thus those with 0,k,0."
> 
> The operator -h,k,-l does NOT take 0,k,0 to its Friedel mate.
> it takes h,0,k to their Friedel mates. In other words the plane
> perpendicular to the 2-fold axis, at 0 along the axis
> 
> Or am I missing something?
> eab
> 
> 
> 
> 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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[ccp4bb] Confused about centric reflections

[Edward A. Berry]

The wiki:

https://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Centric_and_acentric_reflections

says:
"A reflection is centric if there is a reciprocal space symmetry
operator which maps it onto itself (or rather its Friedel mate).
. . .
Centric reflections in space group P2 and P21 are thus those with 0,k,0."

The operator -h,k,-l does NOT take 0,k,0 to its Friedel mate.
it takes h,0,k to their Friedel mates. In other words the plane
perpendicular to the 2-fold axis, at 0 along the axis

Or am I missing something?
eab



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