Re: [ccp4bb] How to define the DNA bond between P and O3’ from two different symmetric units?

[Edward A. Berry]

Dear Peng,
The choice of asymmetric unit is somewhat arbitrary. Please forgive me and 
ignore this if I am saying something obvious and you already know this does not 
apply in your case, but I see most of your previous posts concern EM 
structures, so perhaps you are relatively new to solving x-ray structures?

I assume that you are looking at your structure in coot (or similar), and you 
have turned on the option to show symmetry mates, and you found two places 
where your principal model ends but is continued by a symmetry mate.  If a 
portion of the molecule is visible in symmetry mates, that means it is present 
in your principal model but in a different place- in other words you have built 
parts of two separate molecules.  This is a common result. So you want to find 
out which residues they are, delete them from your main model, and copy then 
from the adjoining symmetry molecule into your main model. You may have to do 
this twice, if your longest stretch is 6BP and there should be 20. But bear in 
mind the second place you observed may be symmetry related, and disappear after 
you fix the first. Possibly some of the molecule is disordered.

There is probably a way to do this all in coot, using things like copy-fragment 
and merge-molecules, but I am a beginner in coot. What you can do is:

Find out which residues you want to transfer from the symmetry mate to main 
model

file:save symmetry coordinates, click on an atom in the symmetry mate where it 
abuts, and give a filename to save it as.

Use a text editor to replace those atoms in your main model with the atoms from 
the symmetry mate (save with a new name just in case)

Load into coot and see if it looks OK

Refine the new model and see if you get essentially statistics equal to before 
and no clashes

The achesymm web server (http://achesym.ibch.poznan.pl/) might be able to do 
this automatically.

(the blind leading the blind - always glad to hear better solutions)

On 01/30/2018 05:41 PM, Peng wrote:


Dear Nicolas,
Thank you for your help.
Our DNA is not a palindromic sequence, and I think it should not be degraded 
easily.
The data can be processed in the space groups C2221, P41212 or lower, with 
12bp, 6bp ,24bp or longer in one NCS. I can see the connection between two 
symmetric DNA molecules in all these space groups.
Actually, I am really confused about that because 20pb-DNA was used in 
crystallization.
Peng




在2018年01月30 16时58分, "Nicolas FOOS"写道:


Dear Peng,

to me your problem sound a bit strange, except if it's a  palindromic 
sequence. I don't understand how you can have one part  of the DNA in one 
asymmetric unit and one in another one. My  question are : maybe you 
considering a NCS as a true symmetry and  underestimate the unit-cell 
dimensions? Or you DNA has been  degraded by DNase and the current size is 
not 20pb, in this case  you are not supposed to create an artificial  
connection. Is the  resolution good enough to be certain of the sequence ?

Sorry, I don't provide any answer, but I am curious and try to  
understand what is going on.

Hope this finally help.

Nicolas

Nicolas Foos
PhD
Structural Biology Group
European Synchrotron Radiation Facility (E.S.R.F)
71, avenue des Martyrs
CS 40220
38043 GRENOBLE Cedex 9
+33 (0)6 76 88 14 87
+33 (0)4 76 88 45 19

On 29/01/2018 20:28, Peng wrote:


Hello, everyone，

 Recently, we solve a protein-DNA complex.20bp-DNA was used for 
crystallization, but only 6bp wasfound in one symmetric unit.

My question is：

How to define the DNA bond between P and O3’from two different 
symmetric units during my refinement?

Peng

Re: [ccp4bb] How to define the DNA bond between P and O3’ from two different symmetric units?

[Peng]

Dear Nicolas,
Thank you for your help.
Our DNA is not a palindromic sequence, and I think it should not be degraded 
easily.
The data can be processed in the space groups C2221, P41212 or lower, with 
12bp, 6bp ,24bp or longer in one NCS. I can see the connection between two 
symmetric DNA molecules in all these space groups. 
Actually, I am really confused about that because 20pb-DNA was used in 
crystallization.
Peng








在2018年01月30 16时58分, "Nicolas FOOS"写道:

 

Dear Peng,

to me your problem sound a bit strange, except if it's a  palindromic 
sequence. I don't understand how you can have one part  of the DNA in one 
asymmetric unit and one in another one. My  question are : maybe you 
considering a NCS as a true symmetry and  underestimate the unit-cell 
dimensions? Or you DNA has been  degraded by DNase and the current size is 
not 20pb, in this case  you are not supposed to create an artificial  
connection. Is the  resolution good enough to be certain of the sequence ?
   

Sorry, I don't provide any answer, but I am curious and try to  understand 
what is going on.
   

Hope this finally help.

Nicolas
   

Nicolas Foos
PhD
Structural Biology Group
European Synchrotron Radiation Facility (E.S.R.F)
71, avenue des Martyrs
CS 40220
38043 GRENOBLE Cedex 9
+33 (0)6 76 88 14 87
+33 (0)4 76 88 45 19
   
On 29/01/2018 20:28, Peng wrote:
   

Hello, everyone，

 Recently, we solve a protein-DNA complex.20bp-DNA was used for 
crystallization, but only 6bp wasfound in one symmetric unit.

My question is： 

How to define the DNA bond between P and O3’from two different 
symmetric units during my refinement?

Peng


   

   

   

 
 

 

   

Re: [ccp4bb] How to define the DNA bond between P and O3’ from two different symmetric units?

[Nicolas FOOS]

Dear Peng,

to me your problem sound a bit strange, except if it's a palindromic 
sequence. I don't understand how you can have one part of the DNA in one 
asymmetric unit and one in another one. My question are : maybe you 
considering a NCS as a true symmetry and underestimate the unit-cell 
dimensions? Or you DNA has been degraded by DNase and the current size 
is not 20pb, in this case you are not supposed to create an artificial  
connection. Is the resolution good enough to be certain of the sequence ?


Sorry, I don't provide any answer, but I am curious and try to 
understand what is going on.


Hope this finally help.

Nicolas

Nicolas Foos
PhD
Structural Biology Group
European Synchrotron Radiation Facility (E.S.R.F)
71, avenue des Martyrs
CS 40220
38043 GRENOBLE Cedex 9
+33 (0)6 76 88 14 87
+33 (0)4 76 88 45 19

On 29/01/2018 20:28, Peng wrote:


Hello, everyone，

 Recently, we solve a protein-DNA complex. 20bp-DNA was used for 
crystallization, but only 6bp was found in one symmetric unit.


My question is：

How to define the DNA bond between P and O3’ from two different 
symmetric units during my refinement?


Peng

[ccp4bb] How to define the DNA bond between P and O3’ from two different symmetric units?

[Peng]

Hello, everyone，

 Recently, we solve a protein-DNA complex. 20bp-DNA was used for 
crystallization, but only 6bp was found in one symmetric unit.

My question is： 

How to define the DNA bond between P and O3’ from two different symmetric units 
during my refinement?

Peng