Re: [ccp4bb] Nitril groups not present on compounds

[Holton, James M]

10% of which beam?

-James Holton
MAD Scientist

On Feb 26, 2019, at 1:38 PM, Maria Håkansson 
mailto:maria.hakans...@saromics.com>> wrote:

Dear all,

We have experienced nitril groups not present in the electron density
after data collection on compounds bound to different proteins.

In one of the projects the compound was tested by MS to check that
the nitril is present in solution before data collection (crystals used to for 
MS analysis).
The nitril should be present since the molecular weight of the compound is the 
same.

Also the crystals have been exposed using 10% of the beam (instead of 100%) to 
try to make
the effect of radiation damage as small as possible. Still the nitril is not 
present.

In both cases the nitril atoms have been modeled with high temperature factors 
but
the electron density is missing, see parts of the compound in the image below 
contoured at 1 sigma level and in a 1.1 Å electron density map.

Has anyone else experienced this?

Best regards,
Maria



Maria Håkansson, PhD, Crystallization Facility Manager
Principal Scientist

SARomics Biostructures AB
Medicon Village
SE-223 81 Lund, Sweden

Mobile: +46 (0)76 8585706
Web: www.saromics.com







To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1

Re: [ccp4bb] Nitril groups not present on compounds

[Mark J van Raaij]

Hi Maria,

from the picture, it looks like disorder to me. Note that the three non-H atoms 
at the top of the ring also have significantly less density than the five non-H 
atoms that are closer to the protein. Perhaps the compounds is just quite 
wobbly in it's binding site.

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
Section Editor of Acta Crystallographica F, Structural Biology Communications
http://journals.iucr.org/f/


> On 26 Feb 2019, at 13:38, Maria Håkansson  
> wrote:
> 
> Dear all,
> 
> We have experienced nitril groups not present in the electron density
> after data collection on compounds bound to different proteins.
> 
> In one of the projects the compound was tested by MS to check that
> the nitril is present in solution before data collection (crystals used to 
> for MS analysis).
> The nitril should be present since the molecular weight of the compound is 
> the same.
> 
> Also the crystals have been exposed using 10% of the beam (instead of 100%) 
> to try to make 
> the effect of radiation damage as small as possible. Still the nitril is not 
> present.
> 
> In both cases the nitril atoms have been modeled with high temperature 
> factors but
> the electron density is missing, see parts of the compound in the image below 
> contoured at 1 sigma level and in a 1.1 Å electron density map.
> 
> Has anyone else experienced this?
> 
> Best regards,
> Maria
>  
> 
> 
> Maria Håkansson, PhD, Crystallization  13.34.17.png>Facility Manager
> Principal Scientist
> 
> SARomics Biostructures AB
> Medicon Village
> SE-223 81 Lund, Sweden
> 
> Mobile: +46 (0)76 8585706
> Web: www.saromics.com 
> 
> 
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 
> 



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1