Re: [ccp4bb] AW: [ccp4bb] NCS difference

[Vipul Panchal]

Hi Schreuder,

Thank you for your suggestion.
As per the electron density, the conformation is very obvious. So I think
whatever NCS outliers are there in structure, are real ones.

Thanking you all,

On 24-Apr-2017 1:29 PM,  wrote:

> Dear Vipul,
>
>
>
> At this resolution and with these Rfactors you are not supposed to
> „correct“ the NCS outliers. Look into the electron density maps if they are
> well defined and if the different conformations can be explained by e.g.
> crystal contacts.
>
>
>
> However, if they are in a less well-defined region, you should superimpose
> the NCS symmetry molecule(s) and see which conformation would fit best and
> fit this conformation in the other molecules as well.
>
>
>
> Best,
>
> Herman
>
>
>
> *Von:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *Im Auftrag von
> *Vipul Panchal
> *Gesendet:* Montag, 24. April 2017 09:49
> *An:* CCP4BB@JISCMAIL.AC.UK
> *Betreff:* [ccp4bb] NCS difference
>
>
>
> Hi all,
>
>
>
> I am solving structure of one of the acyltransferse protein. We have
> collected data at 2.16A resolution. Currently the Rfree is 0.2508 and
> Rwork is 0.2042.
>
>
>
> *My query is regarding NCS difference.* Under validation tool of coot
> while looking for NCS differene, i can find some residues with red bar. *Can
> some one suggest me how may i minimize it if i am expected to do it?*
>
>
>
>
> --
>
> Vipul Panchal
>
> Senior Research Fellow,
>
> Respiratory disease and biology,
>
> CSIR-IGIB
>
> (M)-9540113372
>

[ccp4bb] AW: [ccp4bb] NCS difference

[Herman . Schreuder]

Dear Vipul,

At this resolution and with these Rfactors you are not supposed to „correct“ 
the NCS outliers. Look into the electron density maps if they are well defined 
and if the different conformations can be explained by e.g. crystal contacts.

However, if they are in a less well-defined region, you should superimpose the 
NCS symmetry molecule(s) and see which conformation would fit best and fit this 
conformation in the other molecules as well.

Best,
Herman

Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Vipul 
Panchal
Gesendet: Montag, 24. April 2017 09:49
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [ccp4bb] NCS difference

Hi all,

I am solving structure of one of the acyltransferse protein. We have collected 
data at 2.16A resolution. Currently the Rfree is 0.2508 and Rwork is 0.2042.

My query is regarding NCS difference. Under validation tool of coot while 
looking for NCS differene, i can find some residues with red bar. Can some one 
suggest me how may i minimize it if i am expected to do it?


--
Vipul Panchal
Senior Research Fellow,
Respiratory disease and biology,
CSIR-IGIB
(M)-9540113372