Re: [ccp4bb] Two SGs in one droplet?

[Carter, Charlie]

An arcane, but quite interesting and ultimately functionally relevant 
discussion of this problem can be found here:

L. Kuyper and C. W. Carter, Jr., Resolving Crystal Polymorphisms by finding 
"Stationary Points" from Quantitative Analysis of Crystal Growth Response 
Surfaces, Journal of Crystal Growth 168, 155-169 (1996).

The paper describes how multiple crystal forms from a single drop were resolved 
by studying the conditions under which the crystals of each type grew using 
line search and response surface methods. In the end, crystals of cytidine 
deaminase were shown to grow optimally under at least two different conditions 
that different significantly in the concentration of water. Crystals from the 
dry form are discussed extensively in the literature; that of the wet form is 
described only in this paper. There are 7 extra molecules bound to a dimer 
interface cavity, leading to a modest conformational change in which the dimer 
assumes an asymmetric configuration. It appeared as well that there were 
different active site configurations in the two monomers.

This line of research preoccupied me at some length, and unpublished studies of 
the dependence of log(cat) vs log[H2O] was linear, with a slope of 7, matching 
the number of extra water molecules found in the altered dimer interface. 
Disagreement with Richard Wolfenden over the interpretation of this result, 
together with the fact that the resolution to which the crystals in the wet 
form diffracted prevented us from actually seeing confidently the nature of the 
ligands bound to the two active sites kept this work unpublished, unfortunately.

Charlie

On Oct 28, 2016, at 8:47 AM, Phoebe A. Rice 
<pr...@uchicago.edu<mailto:pr...@uchicago.edu>> wrote:

Back in my grad school days, we had crystals (of gamma delta resolvase large 
fragment) like that: at high protein concentrations, we'd get P6422 with 
1/asymmetric unit, and at lower concentrations, C2221 with 3/asymmetric unit 
(with an imperfect ncs 2fold 60 degrees from the xtal fold, and very similar 
overall packing) that diffracted better.  Sometimes the latter would grow off 
the sides of the former.
 Phoebe

From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@jiscmail.ac.uk>] 
on behalf of Roger Rowlett [rrowl...@colgate.edu<mailto:rrowl...@colgate.edu>]
Sent: Friday, October 28, 2016 9:36 AM
To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@jiscmail.ac.uk>
Subject: Re: [ccp4bb] Two SGs in one droplet?

I've seen this kind of thing before.

Case 1: two crystal forms in the same droplet, C2 and C222. If you looked 
closely, you could tell them apart and I was pretty good at getting a high 
percentage of the desired space group by looking at the crystal forms. The C2 
form diffracted better, so I fished for that one.

Case 2: A mixture of crystals, C2 and C2 with the long axis doubled in length, 
caused by asymmetric ligand binding. In the "double-size" C2 crystal form, 
ligands bound to only 10 of the 12 chains in the double-size ASU, which no 
longer conformed to two adjacent "normal-size" C2 ASUs. In the "normal" size C2 
form, all 6 protein chains in the ASU bound ligand.

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<mailto:rrowl...@colgate.edu>

On 10/28/2016 9:13 AM, Sam Tang wrote:
Dear all

Sorry for going a bit off-topic in this thread.
May I seek your advice as on whether you have experienced that crystals being 
obtained from the same droplet, looking alike under microscope (rod shape) and 
in fact growing possibly from a same nuclei, give two space groups after 
indexing?

I recently obtain crystals for a protein (co-crystallized with a nucleic acid 
ligand) and collected two datasets from synchrotron. Although these two 
crystals are from the same drop, the SG and unit cell dimensions are very 
different:

Xtal1: C121 (156 60 105 90 111 90) (L-test, Pointless shows that there is no 
twinning), ~2.5 Angstrom
Xtal2: P1 (53 60 79 106 105 98), ~3 Angstorm

Would it be possible that the ligand changes the SG of the crystal so that only 
one of the forms contains the ligand?

Any advice is appreciated and thanks a lot in advance for your input.

Regards

Sam Tang
Biochemistry Programme, School of Life Sciences, CUHK

Re: [ccp4bb] Two SGs in one droplet?

[Rangana Sanjeewa]

Hi,

I see this case as an example of Order-Disorder structures. This theory was
developed by Dornburger-Schiff back in 1950s and very well documented.
According to this theory, it is structurally possible to have P1 and C2 (in
this case) and there should be a structural transformation between the two
SPGs (hit: unit cell constants are fairly close as Artem already showed).
Presence of NCS translations are a typical hint for this kind of
structures. Actualy, these strcutures are called polysynthetic twins in the
strcutural chemistry. Also, it may be possible to have other space groups
as well depending on the arrangement of modular layers of protein
molecules, but mostly, the lowest energetic arrangements are ruled out. I
think in this case P1 and C2 structural arrangements are the lowest
energetically favourable arrangements (they are called MDOs, Maximum Degree
of Order strcutures). One way to check this is to look for diffuse
scattering in raw data frames. If you don't see DS, that means that these
structures are MDOs, otherwise non-MDOs.
Now the question be to answered is, what you want from this. If you are
interested in just the protein structure, forget about packing (because,
the modular layer in both cases should be the same). If you want to
establish a relation between the two SPGs, then bit more study would be
needed.

Best,
Rangana


On Mon, Oct 31, 2016 at 7:20 AM, Sam Tang  wrote:

> Dear all
>
> Thanks a lot for the numerous input which is highly appreciated.
>
> I should provide some updates as to what I have done on these two crystals
> / datasets.
>
> I processed both datasets with HKL2000 as well as imosflm. Both softwares
> give (essentially) the same unit cells as in the first email. The C2 cell
> doesn't look like a transformation of the P1 cell.
>
> However Phaser (and in fact Xtriage) identified that there is
> translational pseudosymmetry in the C2 dataset but not the P1 dataset. We
> are lucky enough to obtain MR solutions for the dataset but we remain a bit
> cautious about the C2 we had. Currently we are looking at Zanuda to see if
> this is what it should be.
>
> Thanks again!
>
> Kind regards
>
> Sam
>
>
>
>
> On 30 October 2016 at 14:54, Kevin Jude  wrote:
>
>> 3ICE had two space groups in the same /crystal/ - P6 at one end, P1 with
>> pseudo-6-fold NCS at the other. In the P6 case, the RNA ligand (in the
>> center of a hexameric protein) was rotationally averaged, but in the P1
>> case it could be resolved.
>>
>> Best wishes
>> Kevin
>>
>> On Fri, Oct 28, 2016 at 6:13 AM, Sam Tang  wrote:
>>
>>> Dear all
>>>
>>> Sorry for going a bit off-topic in this thread.
>>> May I seek your advice as on whether you have experienced that crystals
>>> being obtained from the same droplet, looking alike under microscope (rod
>>> shape) and in fact growing possibly from a same nuclei, give two space
>>> groups after indexing?
>>>
>>> I recently obtain crystals for a protein (co-crystallized with a nucleic
>>> acid ligand) and collected two datasets from synchrotron. Although these
>>> two crystals are from the same drop, the SG and unit cell dimensions are
>>> very different:
>>>
>>> Xtal1: C121 (156 60 105 90 111 90) (L-test, Pointless shows that there
>>> is no twinning), ~2.5 Angstrom
>>> Xtal2: P1 (53 60 79 106 105 98), ~3 Angstorm
>>>
>>> Would it be possible that the ligand changes the SG of the crystal so
>>> that only one of the forms contains the ligand?
>>>
>>> Any advice is appreciated and thanks a lot in advance for your input.
>>>
>>> Regards
>>>
>>> Sam Tang
>>> Biochemistry Programme, School of Life Sciences, CUHK
>>>
>>>
>>
>

Re: [ccp4bb] Two SGs in one droplet?

[Sam Tang]

Dear all

Thanks a lot for the numerous input which is highly appreciated.

I should provide some updates as to what I have done on these two crystals
/ datasets.

I processed both datasets with HKL2000 as well as imosflm. Both softwares
give (essentially) the same unit cells as in the first email. The C2 cell
doesn't look like a transformation of the P1 cell.

However Phaser (and in fact Xtriage) identified that there is translational
pseudosymmetry in the C2 dataset but not the P1 dataset. We are lucky
enough to obtain MR solutions for the dataset but we remain a bit cautious
about the C2 we had. Currently we are looking at Zanuda to see if this is
what it should be.

Thanks again!

Kind regards

Sam




On 30 October 2016 at 14:54, Kevin Jude  wrote:

> 3ICE had two space groups in the same /crystal/ - P6 at one end, P1 with
> pseudo-6-fold NCS at the other. In the P6 case, the RNA ligand (in the
> center of a hexameric protein) was rotationally averaged, but in the P1
> case it could be resolved.
>
> Best wishes
> Kevin
>
> On Fri, Oct 28, 2016 at 6:13 AM, Sam Tang  wrote:
>
>> Dear all
>>
>> Sorry for going a bit off-topic in this thread.
>> May I seek your advice as on whether you have experienced that crystals
>> being obtained from the same droplet, looking alike under microscope (rod
>> shape) and in fact growing possibly from a same nuclei, give two space
>> groups after indexing?
>>
>> I recently obtain crystals for a protein (co-crystallized with a nucleic
>> acid ligand) and collected two datasets from synchrotron. Although these
>> two crystals are from the same drop, the SG and unit cell dimensions are
>> very different:
>>
>> Xtal1: C121 (156 60 105 90 111 90) (L-test, Pointless shows that there is
>> no twinning), ~2.5 Angstrom
>> Xtal2: P1 (53 60 79 106 105 98), ~3 Angstorm
>>
>> Would it be possible that the ligand changes the SG of the crystal so
>> that only one of the forms contains the ligand?
>>
>> Any advice is appreciated and thanks a lot in advance for your input.
>>
>> Regards
>>
>> Sam Tang
>> Biochemistry Programme, School of Life Sciences, CUHK
>>
>>
>

Re: [ccp4bb] Two SGs in one droplet?

[Phoebe A. Rice]

Back in my grad school days, we had crystals (of gamma delta resolvase large 
fragment) like that: at high protein concentrations, we'd get P6422 with 
1/asymmetric unit, and at lower concentrations, C2221 with 3/asymmetric unit 
(with an imperfect ncs 2fold 60 degrees from the xtal fold, and very similar 
overall packing) that diffracted better.  Sometimes the latter would grow off 
the sides of the former.
 Phoebe

From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Roger Rowlett 
[rrowl...@colgate.edu]
Sent: Friday, October 28, 2016 9:36 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Two SGs in one droplet?

I've seen this kind of thing before.

Case 1: two crystal forms in the same droplet, C2 and C222. If you looked 
closely, you could tell them apart and I was pretty good at getting a high 
percentage of the desired space group by looking at the crystal forms. The C2 
form diffracted better, so I fished for that one.

Case 2: A mixture of crystals, C2 and C2 with the long axis doubled in length, 
caused by asymmetric ligand binding. In the "double-size" C2 crystal form, 
ligands bound to only 10 of the 12 chains in the double-size ASU, which no 
longer conformed to two adjacent "normal-size" C2 ASUs. In the "normal" size C2 
form, all 6 protein chains in the ASU bound ligand.

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<mailto:rrowl...@colgate.edu>

On 10/28/2016 9:13 AM, Sam Tang wrote:
Dear all

Sorry for going a bit off-topic in this thread.
May I seek your advice as on whether you have experienced that crystals being 
obtained from the same droplet, looking alike under microscope (rod shape) and 
in fact growing possibly from a same nuclei, give two space groups after 
indexing?

I recently obtain crystals for a protein (co-crystallized with a nucleic acid 
ligand) and collected two datasets from synchrotron. Although these two 
crystals are from the same drop, the SG and unit cell dimensions are very 
different:

Xtal1: C121 (156 60 105 90 111 90) (L-test, Pointless shows that there is no 
twinning), ~2.5 Angstrom
Xtal2: P1 (53 60 79 106 105 98), ~3 Angstorm

Would it be possible that the ligand changes the SG of the crystal so that only 
one of the forms contains the ligand?

Any advice is appreciated and thanks a lot in advance for your input.

Regards

Sam Tang
Biochemistry Programme, School of Life Sciences, CUHK

Re: [ccp4bb] Two SGs in one droplet?

[Roger Rowlett]

I've seen this kind of thing before.

Case 1: two crystal forms in the same droplet, C2 and C222. If you 
looked closely, you could tell them apart and I was pretty good at 
getting a high percentage of the desired space group by looking at the 
crystal forms. The C2 form diffracted better, so I fished for that one.


Case 2: A mixture of crystals, C2 and C2 with the long axis doubled in 
length, caused by asymmetric ligand binding. In the "double-size" C2 
crystal form, ligands bound to only 10 of the 12 chains in the 
double-size ASU, which no longer conformed to two adjacent "normal-size" 
C2 ASUs. In the "normal" size C2 form, all 6 protein chains in the ASU 
bound ligand.


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 10/28/2016 9:13 AM, Sam Tang wrote:

Dear all

Sorry for going a bit off-topic in this thread.
May I seek your advice as on whether you have experienced that 
crystals being obtained from the same droplet, looking alike under 
microscope (rod shape) and in fact growing possibly from a same 
nuclei, give two space groups after indexing?


I recently obtain crystals for a protein (co-crystallized with a 
nucleic acid ligand) and collected two datasets from synchrotron. 
Although these two crystals are from the same drop, the SG and unit 
cell dimensions are very different:


Xtal1: C121 (156 60 105 90 111 90) (L-test, Pointless shows that there 
is no twinning), ~2.5 Angstrom

Xtal2: P1 (53 60 79 106 105 98), ~3 Angstorm

Would it be possible that the ligand changes the SG of the crystal so 
that only one of the forms contains the ligand?


Any advice is appreciated and thanks a lot in advance for your input.

Regards

Sam Tang
Biochemistry Programme, School of Life Sciences, CUHK

Re: [ccp4bb] Two SGs in one droplet?

[Harry Powell]

Hi

Something I'd do is try different programs for the indexing to see if you get 
both choices with any programs - Mosflm & XDS will give you the 44 
characteristic lattices and cell parameters by default (so you can easily see 
if anything like the C2 cell is a straightforward transformation of the 
triclinic one), other programs will only give you a selection of the "best" 
choices (by default, anyway). 

But you could just be lucky & get two structures from one crystallisation.

On 28 Oct 2016, at 14:21, Artem Evdokimov wrote:

> Good morning,
> 
> 53 x 2 = 106
> 79 x 2 = 158
> 
> Awfully close to 156 and 105 in the C-group. Are you sure there is no tricky 
> twinning or faulty indexing of some sort - in either of these space group 
> assignments?
> 
> On the other hand, I have seen two different habits and different spacegroups 
> growing from the same drop. So maybe you are just lucky?
> 
> Artem
> www.xtals.org
> 'crystals the size of cats, every time'
> 
> 
> - Cosmic Cats approve of this message
> 
> On Fri, Oct 28, 2016 at 9:13 AM, Sam Tang  wrote:
> Dear all
> 
> Sorry for going a bit off-topic in this thread.
> May I seek your advice as on whether you have experienced that crystals being 
> obtained from the same droplet, looking alike under microscope (rod shape) 
> and in fact growing possibly from a same nuclei, give two space groups after 
> indexing?
> 
> I recently obtain crystals for a protein (co-crystallized with a nucleic acid 
> ligand) and collected two datasets from synchrotron. Although these two 
> crystals are from the same drop, the SG and unit cell dimensions are very 
> different:
> 
> Xtal1: C121 (156 60 105 90 111 90) (L-test, Pointless shows that there is no 
> twinning), ~2.5 Angstrom
> Xtal2: P1 (53 60 79 106 105 98), ~3 Angstorm
> 
> Would it be possible that the ligand changes the SG of the crystal so that 
> only one of the forms contains the ligand?
> 
> Any advice is appreciated and thanks a lot in advance for your input.
> 
> Regards
> 
> Sam Tang
> Biochemistry Programme, School of Life Sciences, CUHK
> 
> 

Harry
--
Dr Harry Powell
Chairman of International Union of Crystallography Commission on 
Crystallographic Computing
Chairman of European Crystallographic Association SIG9 (Crystallographic 
Computing) 

Re: [ccp4bb] Two SGs in one droplet?

[Bert Van-Den-Berg]

It is entirely possible (fairly common) to have two different crystals in one 
drop. If the habits are the same I'd expect the same cell, but that doesn't 
have to be the case. Likewise, if the habits are different I'd expect different 
cells, but again that is not necessarily the case.


bert



From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Sam Tang 
<samtys0...@gmail.com>
Sent: 28 October 2016 14:13
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Two SGs in one droplet?

Dear all

Sorry for going a bit off-topic in this thread.
May I seek your advice as on whether you have experienced that crystals being 
obtained from the same droplet, looking alike under microscope (rod shape) and 
in fact growing possibly from a same nuclei, give two space groups after 
indexing?

I recently obtain crystals for a protein (co-crystallized with a nucleic acid 
ligand) and collected two datasets from synchrotron. Although these two 
crystals are from the same drop, the SG and unit cell dimensions are very 
different:

Xtal1: C121 (156 60 105 90 111 90) (L-test, Pointless shows that there is no 
twinning), ~2.5 Angstrom
Xtal2: P1 (53 60 79 106 105 98), ~3 Angstorm

Would it be possible that the ligand changes the SG of the crystal so that only 
one of the forms contains the ligand?

Any advice is appreciated and thanks a lot in advance for your input.

Regards

Sam Tang
Biochemistry Programme, School of Life Sciences, CUHK

Re: [ccp4bb] Two SGs in one droplet?

[David Briggs]

Hi Sam,

Yes. I've had 2 different crystal forms from the same drop. C2 vs C2221.
Completely different packing, despite that fact that 2 of the cell edges
were within an angstrom or two of each other.
In the above case, I soaked ligand into the crystals, one form had ligand
bound, one didn't, despite the fact that the binding site was available in
both cases.

I think you just need to proceed on a crystal-by-crystal basis and make
zero assumptions during data collection.

HTH,

Dave

On Fri, 28 Oct 2016 at 14:13 Sam Tang  wrote:

> Dear all
>
> Sorry for going a bit off-topic in this thread.
> May I seek your advice as on whether you have experienced that crystals
> being obtained from the same droplet, looking alike under microscope (rod
> shape) and in fact growing possibly from a same nuclei, give two space
> groups after indexing?
>
> I recently obtain crystals for a protein (co-crystallized with a nucleic
> acid ligand) and collected two datasets from synchrotron. Although these
> two crystals are from the same drop, the SG and unit cell dimensions are
> very different:
>
> Xtal1: C121 (156 60 105 90 111 90) (L-test, Pointless shows that there is
> no twinning), ~2.5 Angstrom
> Xtal2: P1 (53 60 79 106 105 98), ~3 Angstorm
>
> Would it be possible that the ligand changes the SG of the crystal so that
> only one of the forms contains the ligand?
>
> Any advice is appreciated and thanks a lot in advance for your input.
>
> Regards
>
> Sam Tang
> Biochemistry Programme, School of Life Sciences, CUHK
>
> --


[image: --]

David Briggs PhD
[image: https://]about.me/david_briggs

Re: [ccp4bb] Two SGs in one droplet?

[Artem Evdokimov]

Good morning,

53 x 2 = 106
79 x 2 = 158

Awfully close to 156 and 105 in the C-group. Are you sure there is no
tricky twinning or faulty indexing of some sort - in either of these space
group assignments?

On the other hand, I have seen two different habits and different
spacegroups growing from the same drop. So maybe you are just lucky?

Artem
www.xtals.org
'crystals the size of cats, *every time*'


- Cosmic Cats approve of this message

On Fri, Oct 28, 2016 at 9:13 AM, Sam Tang  wrote:

> Dear all
>
> Sorry for going a bit off-topic in this thread.
> May I seek your advice as on whether you have experienced that crystals
> being obtained from the same droplet, looking alike under microscope (rod
> shape) and in fact growing possibly from a same nuclei, give two space
> groups after indexing?
>
> I recently obtain crystals for a protein (co-crystallized with a nucleic
> acid ligand) and collected two datasets from synchrotron. Although these
> two crystals are from the same drop, the SG and unit cell dimensions are
> very different:
>
> Xtal1: C121 (156 60 105 90 111 90) (L-test, Pointless shows that there is
> no twinning), ~2.5 Angstrom
> Xtal2: P1 (53 60 79 106 105 98), ~3 Angstorm
>
> Would it be possible that the ligand changes the SG of the crystal so that
> only one of the forms contains the ligand?
>
> Any advice is appreciated and thanks a lot in advance for your input.
>
> Regards
>
> Sam Tang
> Biochemistry Programme, School of Life Sciences, CUHK
>
>

[ccp4bb] Two SGs in one droplet?

[Sam Tang]

Dear all

Sorry for going a bit off-topic in this thread.
May I seek your advice as on whether you have experienced that crystals
being obtained from the same droplet, looking alike under microscope (rod
shape) and in fact growing possibly from a same nuclei, give two space
groups after indexing?

I recently obtain crystals for a protein (co-crystallized with a nucleic
acid ligand) and collected two datasets from synchrotron. Although these
two crystals are from the same drop, the SG and unit cell dimensions are
very different:

Xtal1: C121 (156 60 105 90 111 90) (L-test, Pointless shows that there is
no twinning), ~2.5 Angstrom
Xtal2: P1 (53 60 79 106 105 98), ~3 Angstorm

Would it be possible that the ligand changes the SG of the crystal so that
only one of the forms contains the ligand?

Any advice is appreciated and thanks a lot in advance for your input.

Regards

Sam Tang
Biochemistry Programme, School of Life Sciences, CUHK