Re: [ccp4bb] strange X-ray diffraction diagram――RNA Or Complex？

[Petri Kursula]

From your picture it looks like you have both these needle clusters and single 
needle/rod-lke crystals. The diffraction pattern you show is what you expect 
from a needle cluster (with the ring-like patterns at low resolution), a single 
needle or a larger optimized single crystal should give you no trouble. 

Petri

Petri Kursula, PhD
--
Professor of Biochemistry and Molecular Biology
Department of Biomedicine
University of Bergen, Norway
http://www.uib.no/en/persons/Petri.Kursula 

petri.kurs...@uib.no 
--
Project Leader, Docent
Faculty of Biochemistry and Molecular Medicine
Biocenter Oulu
University of Oulu, Finland
petri.kurs...@oulu.fi 
--



> On 12 Oct 2016, at 08:54, Liu Rachel  wrote:
> 
> 
> Dear everyone:
> 
> Recently, I suffered a problem during my research work. I purified a zinc 
> finger protein, and crystallized as a beautiful cube in a reservoir solution 
> only containing phosphate as the precipitant, no other buffer or molecules. 
> However, regardless of multiple optimization, the crystal diffracted badly 
> (7~8 Å best). I have also tried co-crystallization with dsRNA because this 
> protein can  bind to dsRNA. Then crystals grow in a new condition（2.5M 
> (NH4)2SO4，0.1M BTP,  pH7.0）and its form change to cluster of needle. But the 
> X-ray diffraction diagram is very strange（as shown in the picture）. The Data 
> cannot be processed with HKL2000 either. I want to figure out, could this be 
> a RNA crystal rather than the complex?   Or is there anybody know about the 
> crystal of RNA molecular？
> 
> Thank you very much!
> 
> 
> Yujie Liu 
> Room 2071, research center in life sciences,
> China Agricultural University 
> No. 2 yuanmingyuan west road, Haidian District, Beijing, 100193  P.R. China 
> Tel: (86)-10-62734078
> 
> 

Re: [ccp4bb] strange X-ray diffraction diagram――RNA Or Complex？

[Mark J van Raaij]

Dear Yujie,

At first I thought this looked just like diffraction of multiple salt crystals, 
but there are perhaps a couple of rows of regularly spaced spots from a protein 
crystals. However, I think any program will struggle to get anything useful 
from this. 
Perhaps focussing a small beam (ideally microbeam) on different parts of the 
elongated clusters might get more single-crystal diffraction. 
Seeding using these crystal parts may also yield larger single crystals for 
higher resolution single crystal diffraction...

Greetings,

Mark

PS Anyone agree the crystals look like witches brooms? The stick part of the 
broom may be the single crystal.

Mark J van Raaij
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia - CSIC
calle Darwin 3
E-28049 Madrid, Spain
tel. (+34) 91 585 4616
http://wwwuser.cnb.csic.es/~mjvanraaij







> On 12 Oct 2016, at 08:54, Liu Rachel  wrote:
> 
> 
> Dear everyone:
> 
> Recently, I suffered a problem during my research work. I purified a zinc 
> finger protein, and crystallized as a beautiful cube in a reservoir solution 
> only containing phosphate as the precipitant, no other buffer or molecules. 
> However, regardless of multiple optimization, the crystal diffracted badly 
> (7~8 Å best). I have also tried co-crystallization with dsRNA because this 
> protein can  bind to dsRNA. Then crystals grow in a new condition（2.5M 
> (NH4)2SO4，0.1M BTP,  pH7.0）and its form change to cluster of needle. But the 
> X-ray diffraction diagram is very strange（as shown in the picture）. The Data 
> cannot be processed with HKL2000 either. I want to figure out, could this be 
> a RNA crystal rather than the complex?   Or is there anybody know about the 
> crystal of RNA molecular？
> 
> Thank you very much!
> 
> 
> Yujie Liu 
> Room 2071, research center in life sciences,
> China Agricultural University 
> No. 2 yuanmingyuan west road, Haidian District, Beijing, 100193  P.R. China 
> Tel: (86)-10-62734078
> 
> 

Re: [ccp4bb] strange X-ray diffraction diagram——RNA Or Complex？

[Thomas, Leonard M.]

Yujie,

I would try using another processing program if you have it available, say 
Mosflm.   I look at similar looking diffraction data recently, though without 
the salt crystals mixed in as Herman observed which you also need to take care 
of in the future, and HKL did not handle if very well, Mosflm was able to 
provide a usable data set.  In fairness I have had the reverse  occur also were 
Mosflm was unhappy with the data and HKL gave usable data.

Good Luck.

Leonard M. Thomas Ph.D.
Macromolecular Crystallography Laboratory
Oklahoma COBRE in Structural Biology
Price Family Foundation Institute of Structural Biology
Department of Chemistry and Biochemistry
University of Oklahoma
Stephenson Life Sciences Research Center
101 Stephenson Parkway
Norman, OK 73019
405-325-1126
lmtho...@ou.edu
http://barlywine.chem.ou.edu
http://structuralbiology.ou.edu


From: CCP4 bulletin board  on behalf of 
herman.schreu...@sanofi.com 
Sent: Wednesday, October 12, 2016 2:35:38 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] AW: strange X-ray diffraction diagram——RNA Or Complex？

Dear Yujie,
You have salt crystals in your loop, as evidenced by some very strong 
reflections at high resolution. On the left, at nine o’clock, again at high 
resolution, you have a collection of spots that do not seem to fit to a single 
lattice. Since the low resolution region looks much cleaner, this might again 
be salt or some other small molecule that formed multiple micro crystals.

However, the diffraction at low resolution looks like a bona fide 
macromolecular crystal (protein and/or RNA). What I would do is to apply a 
resolution cut-off and only use the low resolution data for indexing. Once you 
found a good indexing, you could process the data including the high resolution 
data as well.

Good luck!
Herman

Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Liu 
Rachel
Gesendet: Mittwoch, 12. Oktober 2016 08:55
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [ccp4bb] strange X-ray diffraction diagram——RNA Or Complex？




Dear everyone:



Recently, I suffered a problem during my research work. I purified a zinc 
finger protein, and crystallized as a beautiful cube in a reservoir solution 
only containing phosphate as the precipitant, no other buffer or molecules. 
However, regardless of multiple optimization, the crystal diffracted badly (7~8 
Å best). I have also tried co-crystallization with dsRNA because this protein 
can  bind to dsRNA. Then crystals grow in a new condition（2.5M (NH4)2SO4，0.1M 
BTP,  pH7.0）and its form change to cluster of needle. But the X-ray diffraction 
diagram is very strange（as shown in the picture）. The Data cannot be processed 
with HKL2000 either. I want to figure out, could this be a RNA crystal rather 
than the complex?   Or is there anybody know about the crystal of RNA molecular？



Thank you very much!




Yujie Liu

Room 2071, research center in life sciences,

China Agricultural University

No. 2 yuanmingyuan west road, Haidian District, Beijing, 100193  P.R. China

Tel: (86)-10-62734078