Re: [ccp4bb] Strange Diffraction pattern! Protein/DNA complex or DNA alone crystal?

[Philippe BENAS]

Dear Joseph,
I fully agree with Daniel Himmel's answer but you might be able to "index" your 
reflections and get a approximate cell parameters.
I did that in the past with crystals that diffracted very poorly up to 15 
angst. I used HKL200 at that time, cheated with the distance (HKL2000 won't 
accept indexing with too low resolution spots) and selected individual spots 
manually.It was enough for making Matthews analysis for each putative space 
group.The complex formation between the protein and the RNA was confirmed by a 
stoechiometric amount of each macromolecule resulting from OD spectra 
deconvolution taken on dissolved crystals, using a spectrum for the protein 
alone and a spectrum for the RNA alone as references.
Best regards,
Philippe Philippe BENAS, Ph.D.

Laboratoire de Cristallographie et RMN Biologiques, UMR 8015 CNRS
Faculté de Pharmacie, Université Paris Descartes
Case 48
Av, de l'Observatoire
F-75270 PARIS cedex 06
+33.1.5373.1599
E-mails: philippe.be...@parisdescartes.fr, philippe_be...@yahoo.fr
URLs: http://lcrbw.pharmacie.univ-paris5.fr/ , 
http://lcrbw.pharmacie.univ-paris5.fr/spip.php?article18



  De : Joseph Ho <sbddintai...@gmail.com>
 À : CCP4BB@JISCMAIL.AC.UK 
 Envoyé le : Lundi 12 mars 2018 12h54
 Objet : [ccp4bb] Strange Diffraction pattern! Protein/DNA complex or DNA alone 
crystal?
   
Dear all:


I would like to seek your wisdom on our latest diffraction pattern. We
have been working on protein/DNA complex. The protein and DNA have
similar MW. By binding assay, we know the minimal length of DNA. (The
Kd is 0.1-1 microMolar and we can see the complex formation in size
exclusion chromatography up to 200mM NaCl but also some unbound form)
After trying different length of DNA, we recently obtained many
crystal hits (the percipient is either PEG400 or MPD). The final ratio
(prior to protein crystallization) between protein and DNA is 1:1.6
considering some loss of protein during concentration. The crystal is
birefringent. Since high conc. of PEG400 (MPD), the crystals were
directly frozen in liquid N2. However, crystals only diffract to 8-10
angstrom (anisotropic) and also  weird striking line are present
(please see attachment). Do you think if it is  DNA alone crystal or
protein/DNA complex crystal?
How should I improve the diffraction quality?



PS. We have done some tests. For example, set up the same conditions
with DNA alone. I also tried to dissolve crystals in Bradford assay
solution and I believe I saw some blueish color. But none of these
tests are conclusive.

Thanks for your suggestion.

Joseph


   

Re: [ccp4bb] Strange Diffraction pattern! Protein/DNA complex or DNA alone crystal?

[Daniel M. Himmel, Ph. D.]

The diffraction patterns clearly show an overlap of two or more

lattices, which either means you didn’t have a single crystal at the

start or it was damaged during the flash-cooling process.  PEG 400

is generally a good cryoprotectant at ≥20%, but I would recommend using

at least 25% to be certain no ice formation damages the crystal lattice.


The high mosaicity makes interpretation of the diffraction pattern open to

debate.  Some of the reflections look like they could originate from
protein,

since they indicate long distance repeats.  Some double-spots suggest a
cracked

crystal with high mosaicity.  It’s a difficult call for me, but I think the
layer

lines look roughly like an hour glass shape, which is characteristically

seen in DNA patterns and arises from the double-helical structure.

Again, the layer lines suggest at least 2 or 3 lattices.  To pin down

whether you’re really looking at double-helical DNA, you need to

measure the real space distance suggested from layer lines (measure

the equiv. resolution from the reciprocal space origin).  I don’t have

time to look it up now, but there should be tell-tale layer line repeats

(if I recall correctly) at about 10 A and 34 A.  You can look for some

old papers by Francis Crick on helical theory (sorry I don’t have

the reference at my fingertips).  In summary, I would cautiously

surmise that you have a protein (small round spot reflections), bound

by DNA that is much more mobile (highly mosaic layer lines), and that

both the protein and DNA exist in multiple (probably three) lattices, but,

again, the distance repeats of the layer lines have to be measured to

see if they are consistent with double-helical DNA.


Try to get crystals that diffract better for more clarity.  Flash cool in

25% PEG 400 (or try combination of PEG 400 and PEG 200), or

vary the MPD concentration.  Good luck.


I hope this helps.


-Daniel



[image:
RnNZfQn2o2xpggJQqefCOervMbPIci5mujDPJnvl43kv6Rtxjyh5gHN_JKVzeU-aaGz3pePFgxfoAAtZJZNx8mveVTc-11j98EfuAJVcumUenA=s0-d-e1-ft.gif]Daniel
M. Himmel, Ph. D.

URL:  http://www.DanielMHimmel.com 


On Mon, Mar 12, 2018 at 11:24 AM, Joseph Ho  wrote:

> Dear Xiao and Hans:
>
> Thanks for your reply. We tried to index it but failed.
>
> Joseph
> On Mon, Mar 12, 2018 at 11:15 PM, Xiao Lei  wrote:
> > did you try to index it?  the cell dimensions may give you hint.
> >
> > On Mon, Mar 12, 2018 at 4:40 AM, Joseph Ho 
> wrote:
> >>
> >> Dear all:
> >>
> >>
> >> I would like to seek your wisdom on our latest diffraction pattern. We
> >> have been working on protein/DNA complex. The protein and DNA have
> >> similar MW. By binding assay, we know the minimal length of DNA. (The
> >> Kd is 0.1-1 microMolar and we can see the complex formation in size
> >> exclusion chromatography up to 200mM NaCl but also some unbound form)
> >> After trying different length of DNA, we recently obtained many
> >> crystal hits (the percipient is either PEG400 or MPD). The final ratio
> >> (prior to protein crystallization) between protein and DNA is 1:1.6
> >> considering some loss of protein during concentration. The crystal is
> >> birefringent. Since high conc. of PEG400 (MPD), the crystals were
> >> directly frozen in liquid N2. However, crystals only diffract to 8-10
> >> angstrom (anisotropic) and also  weird striking line are present
> >> (please see attachment). Do you think if it is  DNA alone crystal or
> >> protein/DNA complex crystal?
> >> How should I improve the diffraction quality?
> >>
> >>
> >>
> >> PS. We have done some tests. For example, set up the same conditions
> >> with DNA alone. I also tried to dissolve crystals in Bradford assay
> >> solution and I believe I saw some blueish color. But none of these
> >> tests are conclusive.
> >>
> >> Thanks for your suggestion.
> >>
> >> Joseph
> >
> >
>

Re: [ccp4bb] Strange Diffraction pattern! Protein/DNA complex or DNA alone crystal?

[Joseph Ho]

Dear Xiao and Hans:

Thanks for your reply. We tried to index it but failed.

Joseph
On Mon, Mar 12, 2018 at 11:15 PM, Xiao Lei  wrote:
> did you try to index it?  the cell dimensions may give you hint.
>
> On Mon, Mar 12, 2018 at 4:40 AM, Joseph Ho  wrote:
>>
>> Dear all:
>>
>>
>> I would like to seek your wisdom on our latest diffraction pattern. We
>> have been working on protein/DNA complex. The protein and DNA have
>> similar MW. By binding assay, we know the minimal length of DNA. (The
>> Kd is 0.1-1 microMolar and we can see the complex formation in size
>> exclusion chromatography up to 200mM NaCl but also some unbound form)
>> After trying different length of DNA, we recently obtained many
>> crystal hits (the percipient is either PEG400 or MPD). The final ratio
>> (prior to protein crystallization) between protein and DNA is 1:1.6
>> considering some loss of protein during concentration. The crystal is
>> birefringent. Since high conc. of PEG400 (MPD), the crystals were
>> directly frozen in liquid N2. However, crystals only diffract to 8-10
>> angstrom (anisotropic) and also  weird striking line are present
>> (please see attachment). Do you think if it is  DNA alone crystal or
>> protein/DNA complex crystal?
>> How should I improve the diffraction quality?
>>
>>
>>
>> PS. We have done some tests. For example, set up the same conditions
>> with DNA alone. I also tried to dissolve crystals in Bradford assay
>> solution and I believe I saw some blueish color. But none of these
>> tests are conclusive.
>>
>> Thanks for your suggestion.
>>
>> Joseph
>
>

Re: [ccp4bb] Strange diffraction

[Dominika Borek]

Small unit cell and strong diffraction -- I agree with Artem.

D.

Muhammed bashir Khan wrote:
 Hi All;
 I have a strange diffraction pattern from a membrane protein in one of
the
 PEG containing conditions. Could somebody suggest/comments about this
diffraction pattern. Please find the diffraction image attached.
According
 to my experience these are protein crystals but gives a strange
 diffraction.
 Thanks for your help
 Bashir


Dominika Borek, Ph.D. *** UT Southwestern Medical Center
5323 Harry Hines Blvd. *** Dallas, TX 75390-8816
214-645-6378 (phone) *** 214-645-6353 (fax)

Re: [ccp4bb] Strange diffraction image

[Jan Dohnalek]

Could be an organic crystal - what's the resoution of the lowest order
reflections?

Jan D.


On Fri, Oct 12, 2012 at 8:11 AM, Chang Qing robie0...@gmail.com wrote:

 Hi, everyone:

 I just got some strange diffraction images from crystals with
 triangular pyramid shape. I think this should not be protein
 diffraction. I never saw so strange images like this. Does anyone know
 what it is? Is it a kind of salt diffraction?
 Thank you very much

 Chang




-- 
Jan Dohnalek, Ph.D
Institute of Macromolecular Chemistry
Academy of Sciences of the Czech Republic
Heyrovskeho nam. 2
16206 Praha 6
Czech Republic

Tel: +420 296 809 340
Fax: +420 296 809 410

Re: [ccp4bb] RE : [ccp4bb] Strange diffraction image

[Chang Qing]

Hi,
Thanks for answering my question.
I think I'd better provide more informations. These four images were
taken from one crystals. The distance of image1-2 is 250mm, and
image3-4 is 100mm. I checked more than 10 crystals and results were
similar. The spots look very large. The lowest resolution is about 6A.
As my protein can hydrolyze ATP, so protein buffer with 5mM of ATP.
There is 0.2M of MgCl2 in precipitant buffer with PH7.0. 0.06M of CsCl
can improve quality of crystals. I also setup control, in which target
protein was not added, and could get nothing in it. I don't think it
is a protein crystal. But salt spot should not be so large. And the
rings are not just ice-ring. As I got crystal first in hampton crystal
screen kit with MgCl2, TrisHCl and PEG4,000, there are only rings in
images from 5-6A to about 3A.

2012/10/12 THOMPSON Andrew andrew.thomp...@synchrotron-soleil.fr:
 Hi Chang
 No mention of the resolution limit / oscillation range (I think I can see an 
 ice ring, so I would guess 2.5 A?), but it looks like salt to me, with some 
 weaker satellite peaks that may be something weird like an incommensurate 
 phase.
 Did you try to index?
 Cheers
 Andy
 
 De : CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] de la part de Chang Qing 
 [robie0...@gmail.com]
 Date d'envoi : vendredi 12 octobre 2012 08:11
 À : CCP4BB@JISCMAIL.AC.UK
 Objet : [ccp4bb] Strange diffraction image

 Hi, everyone:

 I just got some strange diffraction images from crystals with
 triangular pyramid shape. I think this should not be protein
 diffraction. I never saw so strange images like this. Does anyone know
 what it is? Is it a kind of salt diffraction?
 Thank you very much

 Chang

Re: [ccp4bb] RE : [ccp4bb] Strange diffraction image

[Tim Gruene]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

Dear Chang,

What makes you think spots from salt crystals should not be as large?
You have got an ordinary small molecule crystal  (or probably a
cluster of them) in the beam, with a unit cell somewhat bigger than
that of ice judging by the extra real ice rings you've got.
Hydrolysis of ATP and Mg2+ present - it's probably (Mg)3(PO4)2- it is
very unsoluble http://en.wikipedia.org/wiki/Solubility_table.

Best,
Tim

On 10/12/2012 09:29 AM, Chang Qing wrote:
 Hi, Thanks for answering my question. I think I'd better provide
 more informations. These four images were taken from one crystals.
 The distance of image1-2 is 250mm, and image3-4 is 100mm. I checked
 more than 10 crystals and results were similar. The spots look very
 large. The lowest resolution is about 6A. As my protein can
 hydrolyze ATP, so protein buffer with 5mM of ATP. There is 0.2M of
 MgCl2 in precipitant buffer with PH7.0. 0.06M of CsCl can improve
 quality of crystals. I also setup control, in which target protein
 was not added, and could get nothing in it. I don't think it is a
 protein crystal. But salt spot should not be so large. And the 
 rings are not just ice-ring. As I got crystal first in hampton
 crystal screen kit with MgCl2, TrisHCl and PEG4,000, there are only
 rings in images from 5-6A to about 3A.
 
 2012/10/12 THOMPSON Andrew
 andrew.thomp...@synchrotron-soleil.fr:
 Hi Chang No mention of the resolution limit / oscillation range
 (I think I can see an ice ring, so I would guess 2.5 A?), but it
 looks like salt to me, with some weaker satellite peaks that may
 be something weird like an incommensurate phase. Did you try to
 index? Cheers Andy  De :
 CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] de la part de Chang
 Qing [robie0...@gmail.com] Date d'envoi : vendredi 12 octobre
 2012 08:11 À : CCP4BB@JISCMAIL.AC.UK Objet : [ccp4bb] Strange
 diffraction image
 
 Hi, everyone:
 
 I just got some strange diffraction images from crystals with 
 triangular pyramid shape. I think this should not be protein 
 diffraction. I never saw so strange images like this. Does anyone
 know what it is? Is it a kind of salt diffraction? Thank you very
 much
 
 Chang
 

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

GPG Key ID = A46BEE1A

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Version: GnuPG v1.4.12 (GNU/Linux)
Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/

iD8DBQFQeAheUxlJ7aRr7hoRAibDAJ9yAfiSwNmh8R4tGwUIwFEZno2qWACfStCM
y+xKb+FGGglmv8lTL9Ej8ZQ=
=ub/P
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Re: [ccp4bb] Fwd: [ccp4bb] RE : [ccp4bb] Strange diffraction image

[Nicolas Foos]

Dear Chang,

i have seen ATP diffraction, it's not very different of your image. 
Maybe you have only ATP in your crystals?


Best regard

Nicolas

Le 12/10/12 14:56, Chang Qing a écrit :

Dear Tim

I think your explanation is logical. But I tried ADP as ligand first
and got crystals and diffraction. ATP in additive kit was found to
improve the quality of crystals from cluster to single crystal. CsCl
can go on improving the quality and finally I got crystals like this.
Is it possible that I get some strange crystals such as CsMgCl3 or
something else?
Best regard
Chang

-- Forwarded message --
From: Tim Gruene t...@shelx.uni-ac.gwdg.de
Date: 2012/10/12
Subject: Re: [ccp4bb] RE : [ccp4bb] Strange diffraction image
To: Chang Qing robie0...@gmail.com
抄送： CCP4BB@jiscmail.ac.uk


-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

Dear Chang,

What makes you think spots from salt crystals should not be as large?
You have got an ordinary small molecule crystal  (or probably a
cluster of them) in the beam, with a unit cell somewhat bigger than
that of ice judging by the extra real ice rings you've got.
Hydrolysis of ATP and Mg2+ present - it's probably (Mg)3(PO4)2- it is
very unsoluble http://en.wikipedia.org/wiki/Solubility_table.

Best,
Tim

On 10/12/2012 09:29 AM, Chang Qing wrote:

Hi, Thanks for answering my question. I think I'd better provide
more informations. These four images were taken from one crystals.
The distance of image1-2 is 250mm, and image3-4 is 100mm. I checked
more than 10 crystals and results were similar. The spots look very
large. The lowest resolution is about 6A. As my protein can
hydrolyze ATP, so protein buffer with 5mM of ATP. There is 0.2M of
MgCl2 in precipitant buffer with PH7.0. 0.06M of CsCl can improve
quality of crystals. I also setup control, in which target protein
was not added, and could get nothing in it. I don't think it is a
protein crystal. But salt spot should not be so large. And the
rings are not just ice-ring. As I got crystal first in hampton
crystal screen kit with MgCl2, TrisHCl and PEG4,000, there are only
rings in images from 5-6A to about 3A.

2012/10/12 THOMPSON Andrew
andrew.thomp...@synchrotron-soleil.fr:

Hi Chang No mention of the resolution limit / oscillation range
(I think I can see an ice ring, so I would guess 2.5 A?), but it
looks like salt to me, with some weaker satellite peaks that may
be something weird like an incommensurate phase. Did you try to
index? Cheers Andy  De :
CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] de la part de Chang
Qing [robie0...@gmail.com] Date d'envoi : vendredi 12 octobre
2012 08:11 À : CCP4BB@JISCMAIL.AC.UK Objet : [ccp4bb] Strange
diffraction image

Hi, everyone:

I just got some strange diffraction images from crystals with
triangular pyramid shape. I think this should not be protein
diffraction. I never saw so strange images like this. Does anyone
know what it is? Is it a kind of salt diffraction? Thank you very
much

Chang

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

GPG Key ID = A46BEE1A

-BEGIN PGP SIGNATURE-
Version: GnuPG v1.4.12 (GNU/Linux)
Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/

iD8DBQFQeAheUxlJ7aRr7hoRAibDAJ9yAfiSwNmh8R4tGwUIwFEZno2qWACfStCM
y+xKb+FGGglmv8lTL9Ej8ZQ=
=ub/P
-END PGP SIGNATURE-

Re: [ccp4bb] Fwd: [ccp4bb] RE : [ccp4bb] Strange diffraction image

[Chang Qing]

Dear Nicolas

ATP crystals is a reasonable answer. Thank you very much.

Best regard

Chang

2012/10/12 Nicolas Foos nicolas.f...@afmb.univ-mrs.fr:
 Dear Chang,

 i have seen ATP diffraction, it's not very different of your image. Maybe
 you have only ATP in your crystals?

 Best regard

 Nicolas

 Le 12/10/12 14:56, Chang Qing a écrit :

 Dear Tim

 I think your explanation is logical. But I tried ADP as ligand first
 and got crystals and diffraction. ATP in additive kit was found to
 improve the quality of crystals from cluster to single crystal. CsCl
 can go on improving the quality and finally I got crystals like this.
 Is it possible that I get some strange crystals such as CsMgCl3 or
 something else?
 Best regard
 Chang

 -- Forwarded message --
 From: Tim Gruene t...@shelx.uni-ac.gwdg.de
 Date: 2012/10/12
 Subject: Re: [ccp4bb] RE : [ccp4bb] Strange diffraction image
 To: Chang Qing robie0...@gmail.com
 抄送： CCP4BB@jiscmail.ac.uk


 -BEGIN PGP SIGNED MESSAGE-
 Hash: SHA1

 Dear Chang,

 What makes you think spots from salt crystals should not be as large?
 You have got an ordinary small molecule crystal  (or probably a
 cluster of them) in the beam, with a unit cell somewhat bigger than
 that of ice judging by the extra real ice rings you've got.
 Hydrolysis of ATP and Mg2+ present - it's probably (Mg)3(PO4)2- it is
 very unsoluble http://en.wikipedia.org/wiki/Solubility_table.

 Best,
 Tim

 On 10/12/2012 09:29 AM, Chang Qing wrote:

 Hi, Thanks for answering my question. I think I'd better provide
 more informations. These four images were taken from one crystals.
 The distance of image1-2 is 250mm, and image3-4 is 100mm. I checked
 more than 10 crystals and results were similar. The spots look very
 large. The lowest resolution is about 6A. As my protein can
 hydrolyze ATP, so protein buffer with 5mM of ATP. There is 0.2M of
 MgCl2 in precipitant buffer with PH7.0. 0.06M of CsCl can improve
 quality of crystals. I also setup control, in which target protein
 was not added, and could get nothing in it. I don't think it is a
 protein crystal. But salt spot should not be so large. And the
 rings are not just ice-ring. As I got crystal first in hampton
 crystal screen kit with MgCl2, TrisHCl and PEG4,000, there are only
 rings in images from 5-6A to about 3A.

 2012/10/12 THOMPSON Andrew
 andrew.thomp...@synchrotron-soleil.fr:

 Hi Chang No mention of the resolution limit / oscillation range
 (I think I can see an ice ring, so I would guess 2.5 A?), but it
 looks like salt to me, with some weaker satellite peaks that may
 be something weird like an incommensurate phase. Did you try to
 index? Cheers Andy  De :
 CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] de la part de Chang
 Qing [robie0...@gmail.com] Date d'envoi : vendredi 12 octobre
 2012 08:11 À : CCP4BB@JISCMAIL.AC.UK Objet : [ccp4bb] Strange
 diffraction image

 Hi, everyone:

 I just got some strange diffraction images from crystals with
 triangular pyramid shape. I think this should not be protein
 diffraction. I never saw so strange images like this. Does anyone
 know what it is? Is it a kind of salt diffraction? Thank you very
 much

 Chang

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

 GPG Key ID = A46BEE1A

 -BEGIN PGP SIGNATURE-
 Version: GnuPG v1.4.12 (GNU/Linux)
 Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/

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 y+xKb+FGGglmv8lTL9Ej8ZQ=
 =ub/P
 -END PGP SIGNATURE-

Re: [ccp4bb] Strange diffraction images

[Eleanor Dodson]

Beware twinning tests with pseudo translation! Intensity stats are 
distorted..

What does SFCHECK suggest? It pre-selects data for testing..
 Eeanor

Green, Todd wrote:


I have a case that is similar to this, or at least visually similar by 
diffraction pattern(ie. strong/weak intensities). I think my situation 
is due to a pseudo-translation. I say this my defining of pseudo 
translation as basically something other than pure translation(ie. 
some translation and some degree (albeit slight) of rotation). In my 
case, the crystals (I THINK!) are P23(and i guess you would say pseudo 
I23). There are assemblies at 0,0,0  and 0.5,0.5,0.5. The translated 
assembly at 0.5,0.5,0.5 is slightly misaligned(by a small rotation) 
with the assembly at the origin but near to perfect. If it were 
perfect it'd be I23. But since it is not, it is reduced to the 
Primitive cell. When indexing, if you don't include the more diffuse, 
lower intensity spots, you will lock on the I-cell. If you include 
them then you get right cell, as you would suspect. I included 
pictures. These are 2 regions of a single diffraction pattern with 
spot predictions for the indicated  Bravais lattice. You can easily 
see the sharper more dense spots versus the more diffuse less intense 
ones. In the second shot, you can see that the orthorhombic cell fits 
much better than either of the cubic cells but that's another issue 
which is related to my questions last week. So to muddy the water a 
little, my case could be pseudo-cubic altogether. I'm still working on 
all of that. As a side note, Xtriage doesn't think things are twinned 
as was suggested for one some of the other diffraction patterns 
discussed earlier today.


-Todd




-Original Message-
From: CCP4 bulletin board on behalf of Jacob Keller
Sent: Mon 8/27/2007 10:44 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Strange diffraction images

What a beautiful and interesting diffraction pattern!

To me, it seems that there is a blurred set of spots with different 
cell dimensions, although
nearly the same, underlying the ordered diffraction pattern. A 
possible interpretation occurred to
me, that the ordered part of the crystal is supported by a 
less-ordered lattice of slightly
different dimensions, which, because the crystal is a like a 
layer-cake of 2-d crystals, need not
be commensurable in the short range with the ordered lattice. The 
nicely-ordered cake part of the
crystal you solved, but the frosting between is of a different, less 
ordered nature, giving rise
to the diffuse pattern which has slightly different lattice spacing. I 
would have to see more
images to know whether this apparent lattice-spacing phenomenon is 
consistent, but it at least
seems that way to me from the images you put on the web. I would 
shudder to think of indexing it,

however.

All the best,

Jacob Keller

ps I wonder whether a crystal was ever solved which had two 
interpenetrating, non-commensurable

lattices in it. That would be pretty fantastic.

==Original message text===
On Mon, 27 Aug 2007 5:57:45 am CDT Mark J. van Raaij wrote:

In general, I think we should be careful about too strong statements, 
while in general structures with high solvent diffract to low-res, 
there are a few examples where they diffract to high res. Obviously, 
high solvent content means fewer crystal contacts, but if these few 
are very stable?
Similarly, there are probably a few structures with a high percentage 
of Ramachandran outliers which are real and similarly for all other 
structural quality indicators. However, combinations of various of 
these probably do not exist and in any case, every unusual feature 
like this should be described and an attempt made to explain/analyse 
it, which in the case of the Nature paper that started this thread 
was apparently not done, apart from the rebuttal later (and perhaps 
in unpublished replies to the referees?).


With regards to our structures 1H6W (1.9A) and 1OCY (1.5A), rather 
than faith, I think the structure is held together by a real 
mechanism, which however I can't explain. Like in the structure Axel 
Brunger mentioned, there is appreciable diffuse scatter, which imo 
deserves to be analysed by someone expert in the matter (to whom, or 
anyone else, I would gladly supply the images which I should still 
have on a tape or CD in the cupboard...). For low-res version of one 
image see
http://web.usc.es/~vanraaij/diff45kd.pngand 
http://web.usc.es/%7Evanraaij/diff45kd.pngand
http://web.usc.es/~vanraaij/diff45kdzoom.pngtwo 
http://web.usc.es/%7Evanraaij/diff45kdzoom.pngtwo possibilities I 
have been thinking about:
1. only a few of the tails are ordered, rather like a stack of 
identical tables in which four legs hold the table surfaces stably 
together, but the few ordered tails/legs do not contribute much to 
the diffraction. This raises the question why some tails should be 
stiff and others not; perhaps traces of a metal or other

Re: [ccp4bb] Strange diffraction images

[Boaz Shaanan]

There is also one case of a protein structure that I am aware of, where a 
similar problem has been tackled (the phenomenon is also known as 
one-dimensional disorder, according to A.J.C. Wilson - yes, the one how 
invented the plot).

Check: Trame, CB  mcKay, DB (2001). Acta Cryst. D57, 1079-1090.

  Boaz

- Original Message -
From: George M. Sheldrick [EMAIL PROTECTED]
Date: Monday, August 27, 2007 18:49
Subject: Re: [ccp4bb] Strange diffraction images
To: CCP4BB@JISCMAIL.AC.UK

 Some small molecule crystallographers have specialized in 
 solving and 
 refining structures that, exactly as you describe it, consist of 
 two (or 
 more) interpenetrating, non-commensurable lattices. The usual 
 approach is 
 to decribe the crystal in up to six dimensional space. The 
 programs SAINT 
 and EVALCCD are able to integrate such diffraction patterns and
 SADABS is able to scale them. However the case in point is 
 probably 
 commensurate.
 
 George
 
 Prof. George M. Sheldrick FRS
 Dept. Structural Chemistry, 
 University of Goettingen,
 Tammannstr. 4,
 D37077 Goettingen, Germany
 Tel. +49-551-39-3021 or -3068
 Fax. +49-551-39-2582
 
 
 On Mon, 27 Aug 2007, Jacob Keller wrote:
 
  What a beautiful and interesting diffraction pattern!
  
  To me, it seems that there is a blurred set of spots with 
 different cell dimensions, although
  nearly the same, underlying the ordered diffraction pattern. A 
 possible interpretation occurred to
  me, that the ordered part of the crystal is supported by a 
 less-ordered lattice of slightly
  different dimensions, which, because the crystal is a like a 
 layer-cake of 2-d crystals, need not
  be commensurable in the short range with the ordered lattice. 
 The nicely-ordered cake part of the 
  crystal you solved, but the frosting between is of a 
 different, less ordered nature, giving rise
  to the diffuse pattern which has slightly different lattice 
 spacing. I would have to see more
  images to know whether this apparent lattice-spacing 
 phenomenon is consistent, but it at least
  seems that way to me from the images you put on the web. I 
 would shudder to think of indexing it,
  however.
  
  All the best,
  
  Jacob Keller
  
  ps I wonder whether a crystal was ever solved which had two 
 interpenetrating, non-commensurable
  lattices in it. That would be pretty fantastic.
 
 
 Jacob,
 
 Some small molecule crystallographers have specialized in 
 solving and
 refining structures that, exactly as you describe it, consist of two
 interpenetrating, non-commensurate lattices. The usual approach is
 to index the diffraction pattern in multiple dimensional space 
 ('superspace'). The programs SAINT and EVALCCD are able to 
 integrate 
 diffraction patterns in up to six dimensions, SADABS is able to 
 scale 
 them and the refinement is almost always performed with 
 Petricek's 
 program JANA2000: 
 
 http://www-xray.fzu.cz/jana/Jana2000/jana.html 
 
 However the case in point is probably commensurate.
 
 George
 
 Prof. George M. Sheldrick FRS
 Dept. Structural Chemistry,
 University of Goettingen,
 Tammannstr. 4,
 D37077 Goettingen, Germany
 Tel. +49-551-39-3021 or -3068
 Fax. +49-551-39-2582
 

Boaz Shaanan, Ph.D.
Dept. of Life Sciences
Ben-Gurion University of the Negev
Beer-Sheva 84105
Israel
Phone: 972-8-647-2220 ; Fax: 646-1710
Skype: boaz.shaanan‎

[ccp4bb] AW: [ccp4bb] Strange diffraction images

[Herman . Schreuder]

Dear Todd,
Your diffraction pattern very much looks like suffering from a so-called 
lattice-translocation defect (see e.g. acta cryst D57, 1079; D61, 67 and D61, 
932). In this case, the diffuse spots are caused by stochastic discrete shifts 
between successive layers. Since you do not seem to observe any modulation 
(diffuse spots shifting from e.g. h+k+l even to h+k+l odd for higher h,k,l 
values), the discrete shifts are probably 0.0 and 0.5,0.5,0.5. This means that 
the next layer either packs right on top of the previous layer, or is shifted 
by 0.5,0.5,0.5. If this disorder occurs within coherent range, you get diffuse 
spots.
 
Best regards,
Herman
 





Von: CCP4 bulletin board [mailto:[EMAIL PROTECTED] Im Auftrag von 
Green, Todd
Gesendet: Montag, 27. August 2007 19:49
An: CCP4BB@JISCMAIL.AC.UK
Betreff: Re: [ccp4bb] Strange diffraction images



I have a case that is similar to this, or at least visually similar by 
diffraction pattern(ie. strong/weak intensities). I think my situation is due 
to a pseudo-translation. I say this my defining of pseudo translation as 
basically something other than pure translation(ie. some translation and some 
degree (albeit slight) of rotation). In my case, the crystals (I THINK!) are 
P23(and i guess you would say pseudo I23). There are assemblies at 0,0,0  and 
0.5,0.5,0.5. The translated assembly at 0.5,0.5,0.5 is slightly misaligned(by 
a small rotation) with the assembly at the origin but near to perfect. If it 
were perfect it'd be I23. But since it is not, it is reduced to the Primitive 
cell. When indexing, if you don't include the more diffuse, lower intensity 
spots, you will lock on the I-cell. If you include them then you get right 
cell, as you would suspect. I included pictures. These are 2 regions of a 
single diffraction pattern with spot predictions for the indicated  Bravais 
lattice. You can easily see the sharper more dense spots versus the more 
diffuse less intense ones. In the second shot, you can see that the 
orthorhombic cell fits much better than either of the cubic cells but that's 
another issue which is related to my questions last week. So to muddy the water 
a little, my case could be pseudo-cubic altogether. I'm still working on all of 
that. As a side note, Xtriage doesn't think things are twinned as was suggested 
for one some of the other diffraction patterns discussed earlier today.

-Todd




-Original Message-
From: CCP4 bulletin board on behalf of Jacob Keller
Sent: Mon 8/27/2007 10:44 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Strange diffraction images

What a beautiful and interesting diffraction pattern!

To me, it seems that there is a blurred set of spots with different 
cell dimensions, although
nearly the same, underlying the ordered diffraction pattern. A possible 
interpretation occurred to
me, that the ordered part of the crystal is supported by a less-ordered 
lattice of slightly
different dimensions, which, because the crystal is a like a layer-cake 
of 2-d crystals, need not
be commensurable in the short range with the ordered lattice. The 
nicely-ordered cake part of the
crystal you solved, but the frosting between is of a different, less 
ordered nature, giving rise
to the diffuse pattern which has slightly different lattice spacing. I 
would have to see more
images to know whether this apparent lattice-spacing phenomenon is 
consistent, but it at least
seems that way to me from the images you put on the web. I would 
shudder to think of indexing it,
however.

All the best,

Jacob Keller

ps I wonder whether a crystal was ever solved which had two 
interpenetrating, non-commensurable
lattices in it. That would be pretty fantastic.

==Original message text===
On Mon, 27 Aug 2007 5:57:45 am CDT Mark J. van Raaij wrote:

In general, I think we should be careful about too strong statements, 
while in general structures with high solvent diffract to low-res, 
there are a few examples where they diffract to high res. Obviously, 
high solvent content means fewer crystal contacts, but if these few 
are very stable?
Similarly, there are probably a few structures with a high percentage 
of Ramachandran outliers which are real and similarly for all other 
structural quality indicators. However, combinations of various of 
these probably do not exist and in any case, every unusual feature 
like this should be described and an attempt made to explain/analyse 
it, which in the case of the Nature paper that started this thread

[ccp4bb] Strange diffraction images

[Jacob Keller]

What a beautiful and interesting diffraction pattern!

To me, it seems that there is a blurred set of spots with different cell 
dimensions, although
nearly the same, underlying the ordered diffraction pattern. A possible 
interpretation occurred to
me, that the ordered part of the crystal is supported by a less-ordered lattice 
of slightly
different dimensions, which, because the crystal is a like a layer-cake of 2-d 
crystals, need not
be commensurable in the short range with the ordered lattice. The 
nicely-ordered cake part of the 
crystal you solved, but the frosting between is of a different, less ordered 
nature, giving rise
to the diffuse pattern which has slightly different lattice spacing. I would 
have to see more
images to know whether this apparent lattice-spacing phenomenon is consistent, 
but it at least
seems that way to me from the images you put on the web. I would shudder to 
think of indexing it,
however.

All the best,

Jacob Keller

ps I wonder whether a crystal was ever solved which had two interpenetrating, 
non-commensurable
lattices in it. That would be pretty fantastic.

==Original message text===
On Mon, 27 Aug 2007 5:57:45 am CDT Mark J. van Raaij wrote:

In general, I think we should be careful about too strong statements,  
while in general structures with high solvent diffract to low-res,  
there are a few examples where they diffract to high res. Obviously,  
high solvent content means fewer crystal contacts, but if these few  
are very stable?
Similarly, there are probably a few structures with a high percentage  
of Ramachandran outliers which are real and similarly for all other  
structural quality indicators. However, combinations of various of  
these probably do not exist and in any case, every unusual feature  
like this should be described and an attempt made to explain/analyse  
it, which in the case of the Nature paper that started this thread  
was apparently not done, apart from the rebuttal later (and perhaps  
in unpublished replies to the referees?).

With regards to our structures 1H6W (1.9A) and 1OCY (1.5A), rather  
than faith, I think the structure is held together by a real  
mechanism, which however I can't explain. Like in the structure Axel  
Brunger mentioned, there is appreciable diffuse scatter, which imo  
deserves to be analysed by someone expert in the matter (to whom, or  
anyone else, I would gladly supply the images which I should still  
have on a tape or CD in the cupboard...). For low-res version of one  
image see
http://web.usc.es/~vanraaij/diff45kd.pngand
http://web.usc.es/~vanraaij/diff45kdzoom.pngtwo possibilities I have been 
thinking about:
1. only a few of the tails are ordered, rather like a stack of  
identical tables in which four legs hold the table surfaces stably  
together, but the few ordered tails/legs do not contribute much to  
the diffraction. This raises the question why some tails should be  
stiff and others not; perhaps traces of a metal or other small  
molecule stabilise some tails (although crystal optimisation trials  
did not show up such a molecule)?
2. three-fold disorder, either individually or in microdomains too  
small to have been resolved by the beam used. For this I have been  
told to expect better density than observed, but maybe this is not true.
we did try integrating in lower space groups P3, P2 instead of P321  
with no improvement of the density, we tried a RT dataset to see if  
freezing caused the disorder and we tried improving the phases by MAD  
on the mercury derivative, but with no improvement in the density for  
the tail.

Mark J. van Raaij
Unidad de Bioquímica Estructural
Dpto de Bioquímica, Facultad de Farmacia
and
Unidad de Rayos X, Edificio CACTUS
Universidad de Santiago
15782 Santiago de Compostela
Spain
http://web.usc.es/~vanraaij/

On 24 Aug 2007, at 03:01, Petr Leiman wrote:

 - Original Message - From: Jenny Martin  
 [EMAIL PROTECTED]
 To: CCP4BB@JISCMAIL.AC.UK
 Sent: Thursday, August 23, 2007 5:46 PM
 Subject: Re: [ccp4bb] The importance of USING our validation tools

 My question is, how could crystals with 80% or more solvent  
 diffract  so well? The best of the three is 1.9A resolution with I/ 
 sigI 48 (top  shell 2.5). My experience is that such crystals  
 diffract very weakly.

 You must be thinking about Mark van Raaij's T4 short tail fibre  
 structures. Yes, the disorder in those crystals is extreme. There  
 are ~100-150 A thick disordered layers between the ~200 A thick  
 layers of ordered structure. The diffraction pattern does not show  
 any anomalies (as far as I can remember from 6 years ago). The  
 spots are round, there are virtually no spots not covered by  
 predictions, and the crystals diffract to 1.5A resolution. The  
 disordered layers are perpendicular to the threefold axis of the  
 crystal. The molecule is a trimer and sits on the threefold axis.  
 It appears that the ordered layers somehow know how to 

Re: [ccp4bb] Strange diffraction images

[George M. Sheldrick]

Some small molecule crystallographers have specialized in solving and 
refining structures that, exactly as you describe it, consist of two (or 
more) interpenetrating, non-commensurable lattices. The usual approach is 
to decribe the crystal in up to six dimensional space. The programs SAINT 
and EVALCCD are able to integrate such diffraction patterns and
SADABS is able to scale them. However the case in point is probably 
commensurate.

George

Prof. George M. Sheldrick FRS
Dept. Structural Chemistry, 
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-3021 or -3068
Fax. +49-551-39-2582


On Mon, 27 Aug 2007, Jacob Keller wrote:

 What a beautiful and interesting diffraction pattern!
 
 To me, it seems that there is a blurred set of spots with different cell 
 dimensions, although
 nearly the same, underlying the ordered diffraction pattern. A possible 
 interpretation occurred to
 me, that the ordered part of the crystal is supported by a less-ordered 
 lattice of slightly
 different dimensions, which, because the crystal is a like a layer-cake of 
 2-d crystals, need not
 be commensurable in the short range with the ordered lattice. The 
 nicely-ordered cake part of the 
 crystal you solved, but the frosting between is of a different, less 
 ordered nature, giving rise
 to the diffuse pattern which has slightly different lattice spacing. I would 
 have to see more
 images to know whether this apparent lattice-spacing phenomenon is 
 consistent, but it at least
 seems that way to me from the images you put on the web. I would shudder to 
 think of indexing it,
 however.
 
 All the best,
 
 Jacob Keller
 
 ps I wonder whether a crystal was ever solved which had two interpenetrating, 
 non-commensurable
 lattices in it. That would be pretty fantastic.


Jacob,

Some small molecule crystallographers have specialized in solving and
refining structures that, exactly as you describe it, consist of two
interpenetrating, non-commensurate lattices. The usual approach is
to index the diffraction pattern in multiple dimensional space 
('superspace'). The programs SAINT and EVALCCD are able to integrate 
diffraction patterns in up to six dimensions, SADABS is able to scale 
them and the refinement is almost always performed with Petricek's 
program JANA2000: 

http://www-xray.fzu.cz/jana/Jana2000/jana.html 

However the case in point is probably commensurate.

George

Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-3021 or -3068
Fax. +49-551-39-2582

Re: [ccp4bb] Strange diffraction images

[Jacob Keller]

I am still eagerly awaiting a biomacromolecular quasicrystal with a five-fold 
symmetric diffraction 
pattern. It seems that this is entirely possible, if one gets roughly 
Penrose-tile shaped oligomers 
somehow. But wow, how would you solve that thing? I guess one would have to 
modify software from
the small molecule or matsci folks.

Jacob


==Original message text===
On Mon, 27 Aug 2007 11:19:15 am CDT George M. Sheldrick wrote:


Some small molecule crystallographers have specialized in solving and 
refining structures that, exactly as you describe it, consist of two (or 
more) interpenetrating, non-commensurable lattices. The usual approach is 
to decribe the crystal in up to six dimensional space. The programs SAINT 
and EVALCCD are able to integrate such diffraction patterns and
SADABS is able to scale them. However the case in point is probably 
commensurate.

George

Prof. George M. Sheldrick FRS
Dept. Structural Chemistry, 
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-3021 or -3068
Fax. +49-551-39-2582


On Mon, 27 Aug 2007, Jacob Keller wrote:

 What a beautiful and interesting diffraction pattern!
 
 To me, it seems that there is a blurred set of spots with different cell 
 dimensions, although
 nearly the same, underlying the ordered diffraction pattern. A possible 
 interpretation occurred to
 me, that the ordered part of the crystal is supported by a less-ordered 
 lattice of slightly
 different dimensions, which, because the crystal is a like a layer-cake of 
 2-d crystals, need not
 be commensurable in the short range with the ordered lattice. The 
 nicely-ordered cake part of the 
 crystal you solved, but the frosting between is of a different, less 
 ordered nature, giving rise
 to the diffuse pattern which has slightly different lattice spacing. I would 
 have to see more
 images to know whether this apparent lattice-spacing phenomenon is 
 consistent, but it at least
 seems that way to me from the images you put on the web. I would shudder to 
 think of indexing it,
 however.
 
 All the best,
 
 Jacob Keller
 
 ps I wonder whether a crystal was ever solved which had two interpenetrating, 
 non-commensurable
 lattices in it. That would be pretty fantastic.


Jacob,

Some small molecule crystallographers have specialized in solving and
refining structures that, exactly as you describe it, consist of two
interpenetrating, non-commensurate lattices. The usual approach is
to index the diffraction pattern in multiple dimensional space 
('superspace'). The programs SAINT and EVALCCD are able to integrate 
diffraction patterns in up to six dimensions, SADABS is able to scale 
them and the refinement is almost always performed with Petricek's 
program JANA2000: 

http://www-xray.fzu.cz/jana/Jana2000/jana.html 
However the case in point is probably commensurate.

George

Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-3021 or -3068
Fax. +49-551-39-2582
===End of original message text===



***
Jacob Keller
Northwestern University
6541 N. Francisco #3
Chicago IL 60645
(847)467-4049
[EMAIL PROTECTED]
***

Re: [ccp4bb] Strange diffraction images - PS

[George M. Sheldrick]

Apologies, part of my previous message was missing and part 
appeared twice. Here is another try:

Jacob,

Some small molecule crystallographers have specialized in solving and
refining structures that, exactly as you describe it, consist of two
interpenetrating, non-commensurate lattices. The usual approach is
to index the diffraction pattern in multiple dimensional space
('superspace'). The programs SAINT and EVALCCD are able to integrate
diffraction patterns in up to six dimensions, SADABS is able to scale
them and the refinement is almost always performed with Petricek's
program JANA2000:

http://www-xray.fzu.cz/jana/Jana2000/jana.html

However the case in point is probably commensurate.

George


Prof. George M. Sheldrick FRS
Dept. Structural Chemistry, 
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-3021 or -3068
Fax. +49-551-39-2582

Re: [ccp4bb] Strange diffraction images

[Raji Edayathumangalam]

Very dumb question perhaps:

If there were two interpenetrating lattices of slightly different cell 
dimensions, would we not
expect that the indexing program would leave out a lot of the spots as 
unpredicted or uncovered?

Could someone clarify with respect to the diffraction pattern that has just 
been posted (diff45..png)?

Raji



-Included Message--
Some small molecule crystallographers have specialized in solving and 
refining structures that, exactly as you describe it, consist of two (or 
more) interpenetrating, non-commensurable lattices. The usual approach is 
to decribe the crystal in up to six dimensional space. The programs SAINT 
and EVALCCD are able to integrate such diffraction patterns and
SADABS is able to scale them. However the case in point is probably 
commensurate.

George

Prof. George M. Sheldrick FRS
Dept. Structural Chemistry, 
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-3021 or -3068
Fax. +49-551-39-2582


On Mon, 27 Aug 2007, Jacob Keller wrote:

 What a beautiful and interesting diffraction pattern!
 
 To me, it seems that there is a blurred set of spots with different cell 
 dimensions, although
 nearly the same, underlying the ordered diffraction pattern. A possible 
 interpretation occurred to
 me, that the ordered part of the crystal is supported by a less-ordered 
 lattice of slightly
 different dimensions, which, because the crystal is a like a layer-cake of 
 2-d crystals, need not
 be commensurable in the short range with the ordered lattice. The 
 nicely-ordered cake part of the 
 crystal you solved, but the frosting between is of a different, less 
 ordered nature, giving rise
 to the diffuse pattern which has slightly different lattice spacing. I would 
 have to see more
 images to know whether this apparent lattice-spacing phenomenon is 
 consistent, but it at least
 seems that way to me from the images you put on the web. I would shudder to 
 think of indexing it,
 however.
 
 All the best,
 
 Jacob Keller
 
 ps I wonder whether a crystal was ever solved which had two 
 interpenetrating, non-commensurable
 lattices in it. That would be pretty fantastic.


Jacob,

Some small molecule crystallographers have specialized in solving and
refining structures that, exactly as you describe it, consist of two
interpenetrating, non-commensurate lattices. The usual approach is
to index the diffraction pattern in multiple dimensional space 
('superspace'). The programs SAINT and EVALCCD are able to integrate 
diffraction patterns in up to six dimensions, SADABS is able to scale 
them and the refinement is almost always performed with Petricek's 
program JANA2000: 

http://www-xray.fzu.cz/jana/Jana2000/jana.html 

However the case in point is probably commensurate.

George

Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-3021 or -3068
Fax. +49-551-39-2582


-End of Included Message--

Re: [ccp4bb] Strange diffraction images

[Jacob Keller]

The left-out spots would be the diffuse spots, which I assume were not 
indexed/integrated. The
sharp spots were presumably used to solve the structure.

JPK


==Original message text===
On Mon, 27 Aug 2007 11:36:08 am CDT Raji Edayathumangalam wrote:

Very dumb question perhaps:

If there were two interpenetrating lattices of slightly different cell 
dimensions, would we not
expect that the indexing program would leave out a lot of the spots as 
unpredicted or uncovered?

Could someone clarify with respect to the diffraction pattern that has just 
been posted (diff45..png)?

Raji



-Included Message--
Some small molecule crystallographers have specialized in solving and 
refining structures that, exactly as you describe it, consist of two (or 
more) interpenetrating, non-commensurable lattices. The usual approach is 
to decribe the crystal in up to six dimensional space. The programs SAINT 
and EVALCCD are able to integrate such diffraction patterns and
SADABS is able to scale them. However the case in point is probably 
commensurate.

George

Prof. George M. Sheldrick FRS
Dept. Structural Chemistry, 
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-3021 or -3068
Fax. +49-551-39-2582


On Mon, 27 Aug 2007, Jacob Keller wrote:

 What a beautiful and interesting diffraction pattern!
 
 To me, it seems that there is a blurred set of spots with different cell 
 dimensions, although
 nearly the same, underlying the ordered diffraction pattern. A possible 
 interpretation occurred to
 me, that the ordered part of the crystal is supported by a less-ordered 
 lattice of slightly
 different dimensions, which, because the crystal is a like a layer-cake of 
 2-d crystals, need not
 be commensurable in the short range with the ordered lattice. The 
 nicely-ordered cake part of the 
 crystal you solved, but the frosting between is of a different, less 
 ordered nature, giving rise
 to the diffuse pattern which has slightly different lattice spacing. I would 
 have to see more
 images to know whether this apparent lattice-spacing phenomenon is 
 consistent, but it at least
 seems that way to me from the images you put on the web. I would shudder to 
 think of indexing it,
 however.
 
 All the best,
 
 Jacob Keller
 
 ps I wonder whether a crystal was ever solved which had two 
 interpenetrating, non-commensurable
 lattices in it. That would be pretty fantastic.


Jacob,

Some small molecule crystallographers have specialized in solving and
refining structures that, exactly as you describe it, consist of two
interpenetrating, non-commensurate lattices. The usual approach is
to index the diffraction pattern in multiple dimensional space 
('superspace'). The programs SAINT and EVALCCD are able to integrate 
diffraction patterns in up to six dimensions, SADABS is able to scale 
them and the refinement is almost always performed with Petricek's 
program JANA2000: 

http://www-xray.fzu.cz/jana/Jana2000/jana.html 
However the case in point is probably commensurate.

George

Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-3021 or -3068
Fax. +49-551-39-2582


-End of Included Message--
===End of original message text===



***
Jacob Keller
Northwestern University
6541 N. Francisco #3
Chicago IL 60645
(847)467-4049
[EMAIL PROTECTED]
***

Re: [ccp4bb] Strange diffraction images

[Peter Zwart]

 As a side note, Xtriage
 doesn't think things are twinned as was suggested for one some of the other
 diffraction patterns discussed earlier today.

Hi Todd,

Detection of twinning in the presence of pseudo translations / and or
NCS parallel to the twin law is difficult and using model based
techniques (RvsR statistic) could be usefull.

Furthermore, I would like to point to Acta D 63, 926-930 with some
pointers to literature regaring other 'weird' pathologies.


HTH

Peter

Re: [ccp4bb] Strange diffraction images

[Bart Hazes]

I believe Wayne Hendrickson's lab has had such a case with a 10-fold 
symmetric mollusc hemocyanin crystal. This must have been in the early 
90's and to my knowlwedge they were never able to solve the structure 
even though it diffracted beyond 2 Anstrom.


I'm not sure if this work has been published but you can check the paper 
describing a single domain of this protein complex or contact one of its 
authors.


Bart

J Mol Biol. 1998 May 15;278(4):855-70.

Crystal structure of a functional unit from Octopus hemocyanin.
Cuff ME, Miller KI, van Holde KE, Hendrickson WA.

Jacob Keller wrote:
I am still eagerly awaiting a biomacromolecular quasicrystal with a five-fold symmetric diffraction 
pattern. It seems that this is entirely possible, if one gets roughly Penrose-tile shaped oligomers 
somehow. But wow, how would you solve that thing? I guess one would have to modify software from

the small molecule or matsci folks.

Jacob


==Original message text===
On Mon, 27 Aug 2007 11:19:15 am CDT George M. Sheldrick wrote:


Some small molecule crystallographers have specialized in solving and 
refining structures that, exactly as you describe it, consist of two (or 
more) interpenetrating, non-commensurable lattices. The usual approach is 
to decribe the crystal in up to six dimensional space. The programs SAINT 
and EVALCCD are able to integrate such diffraction patterns and
SADABS is able to scale them. However the case in point is probably 
commensurate.


George

Prof. George M. Sheldrick FRS
Dept. Structural Chemistry, 
University of Goettingen,

Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-3021 or -3068
Fax. +49-551-39-2582


On Mon, 27 Aug 2007, Jacob Keller wrote:



What a beautiful and interesting diffraction pattern!

To me, it seems that there is a blurred set of spots with different cell 
dimensions, although
nearly the same, underlying the ordered diffraction pattern. A possible 
interpretation occurred to
me, that the ordered part of the crystal is supported by a less-ordered lattice 
of slightly
different dimensions, which, because the crystal is a like a layer-cake of 2-d 
crystals, need not
be commensurable in the short range with the ordered lattice. The nicely-ordered cake part of the 
crystal you solved, but the frosting between is of a different, less ordered nature, giving rise

to the diffuse pattern which has slightly different lattice spacing. I would 
have to see more
images to know whether this apparent lattice-spacing phenomenon is consistent, 
but it at least
seems that way to me from the images you put on the web. I would shudder to 
think of indexing it,
however.

All the best,

Jacob Keller

ps I wonder whether a crystal was ever solved which had two interpenetrating, 
non-commensurable
lattices in it. That would be pretty fantastic.




Jacob,

Some small molecule crystallographers have specialized in solving and
refining structures that, exactly as you describe it, consist of two
interpenetrating, non-commensurate lattices. The usual approach is
to index the diffraction pattern in multiple dimensional space 
('superspace'). The programs SAINT and EVALCCD are able to integrate 
diffraction patterns in up to six dimensions, SADABS is able to scale 
them and the refinement is almost always performed with Petricek's 
program JANA2000: 

http://www-xray.fzu.cz/jana/Jana2000/jana.html 
However the case in point is probably commensurate.


George

Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-3021 or -3068
Fax. +49-551-39-2582
===End of original message text===



***
Jacob Keller
Northwestern University
6541 N. Francisco #3
Chicago IL 60645
(847)467-4049
[EMAIL PROTECTED]
***





--

==

Bart Hazes (Assistant Professor)
Dept. of Medical Microbiology  Immunology
University of Alberta
1-15 Medical Sciences Building
Edmonton, Alberta
Canada, T6G 2H7
phone:  1-780-492-0042
fax:1-780-492-7521

==

Re: [ccp4bb] Strange diffraction images

[Jacob Keller]

I think if there had been a case of a protein quasicrystal, it would have made 
the cover of Nature

Here are some papers about quasicrystals:

1: Proc Natl Acad Sci U S A. 1996 Dec 10;93(25):14267-70.

New perspectives on forbidden symmetries, quasicrystals, and Penrose 
tilings.
Steinhardt PJ.

Quasicrystals are solids with quasiperiodic atomic structures and 
symmetries forbidden to
ordinary periodic crystals-e.g., 5-fold symmetry axes. A powerful model for 
understanding their
structure and properties has been the two-dimensional Penrose tiling. Recently 
discovered
properties of Penrose tilings suggest a simple picture of the structure of 
quasicrystals and shed
new light on why they form. The results show that quasicrystals can be 
constructed from a single
repeating cluster of atoms and that the rigid matching rules of Penrose tilings 
can be replaced by
more physically plausible cluster energetics. The new concepts make the 
conditions for forming
quasicrystals appear to be closely related to the conditions for forming 
periodic crystals.

2: Proc Natl Acad Sci U S A. 1996 Dec 10;93(25):14271-8.

Five-fold symmetry in crystalline quasicrystal lattices.
Caspar DL, Fontano E.

Institute of Molecular Biophysics, Florida State University, Tallahassee, 
32306-3015, USA.
[EMAIL PROTECTED]

To demonstrate that crystallographic methods can be applied to index and 
interpret diffraction
patterns from well-ordered quasicrystals that display non-crystallographic 
5-fold symmetry, we have 
characterized the properties of a series of periodic two-dimensional lattices 
built from pentagons, 
called Fibonacci pentilings, which resemble aperiodic Penrose tilings. The 
computed diffraction
patterns from periodic pentilings with moderate size unit cells show decagonal 
symmetry and are
virtually indistinguishable from that of the infinite aperiodic pentiling. We 
identify the vertices 
and centers of the pentagons forming the pentiling with the positions of 
transition metal atoms
projected on the plane perpendicular to the decagonal axis of quasicrystals 
whose structure is
related to crystalline eta phase alloys. The characteristic length scale of the 
pentiling lattices, 
evident from the Patterson (autocorrelation) function, is approximately tau 2 
times the pentagon
edge length, where tau is the golden ratio. Within this distance there are a 
finite number of local 
atomic motifs whose structure can be crystallographically refined against the 
experimentally
measured diffraction data.


Jacob

==Original message text===
On Mon, 27 Aug 2007 2:02:36 pm CDT Bart Hazes wrote:

I believe Wayne Hendrickson's lab has had such a case with a 10-fold 
symmetric mollusc hemocyanin crystal. This must have been in the early 
90's and to my knowlwedge they were never able to solve the structure 
even though it diffracted beyond 2 Anstrom.

I'm not sure if this work has been published but you can check the paper 
describing a single domain of this protein complex or contact one of its 
authors.

Bart

J Mol Biol. 1998 May 15;278(4):855-70.

Crystal structure of a functional unit from Octopus hemocyanin.
Cuff ME, Miller KI, van Holde KE, Hendrickson WA.

Jacob Keller wrote:
 I am still eagerly awaiting a biomacromolecular quasicrystal with a five-fold 
 symmetric diffraction 
 pattern. It seems that this is entirely possible, if one gets roughly 
 Penrose-tile shaped oligomers 
 somehow. But wow, how would you solve that thing? I guess one would have to 
 modify software from
 the small molecule or matsci folks.
 
 Jacob
 
 
 ==Original message text===
 On Mon, 27 Aug 2007 11:19:15 am CDT George M. Sheldrick wrote:
 
 
 Some small molecule crystallographers have specialized in solving and 
 refining structures that, exactly as you describe it, consist of two (or 
 more) interpenetrating, non-commensurable lattices. The usual approach is 
 to decribe the crystal in up to six dimensional space. The programs SAINT 
 and EVALCCD are able to integrate such diffraction patterns and
 SADABS is able to scale them. However the case in point is probably 
 commensurate.
 
 George
 
 Prof. George M. Sheldrick FRS
 Dept. Structural Chemistry, 
 University of Goettingen,
 Tammannstr. 4,
 D37077 Goettingen, Germany
 Tel. +49-551-39-3021 or -3068
 Fax. +49-551-39-2582
 
 
 On Mon, 27 Aug 2007, Jacob Keller wrote:
 
 
What a beautiful and interesting diffraction pattern!

To me, it seems that there is a blurred set of spots with different cell 
dimensions, although
nearly the same, underlying the ordered diffraction pattern. A possible 
interpretation occurred to
me, that the ordered part of the crystal is supported by a less-ordered 
lattice of slightly
different dimensions, which, because the crystal is a like a layer-cake of 
2-d crystals, need not
be commensurable in the short range with the ordered lattice. The 
nicely-ordered cake part of the 
crystal you