On Thursday, 23 April, 2015 18:25:35 Gert Bange wrote:
> Dear Mishba,
>
> Just check density vs model by simply open 'Coot',
>
> Go to: 'File' -> 'Fetch PDB & Map using EDS'
>
> Type the pdb entry into the field - enjoy the densities.
If you want to pursue the plausibility of specific outliers
you could also download and superimpose PDB entry 1LMB
(deposited in 1993, 15 years earlier) and calculate a "Kleywegt plot"
comparing the difference in phi/psi between the two structures
at each residue they share. This is in the "validation" menu of Coot.
Compare the models at their points of difference and
decide for yourself.
1LMB has 0% phi/psi outliers, though it contains a smaller
piece of the structure. If you care to dig deeper,
you could re-refine 3BDN after substituting the 1LMB coordinates
for the 3BDN coordinates in the region where the chains
superimpose well.
I have not looked at any of the other related PDB structures,
but you would want investigate those as well.
Ethan
>
> Best and god save the EDS,
>
> Gert
>
>
> -----------------------------------------------------
> LOEWE Center for Synthetic Microbiology
> AG Bange - Analysis of Metabolic Networks
> Dr. Gert Bange
> Hans-Meerwein-Strasse, C7
> 35043 Marburg, Germany
> office: +49-6421-28-23361
> fax: +49-6421-28-24430
> web: www.synmikro.com/bange
> -----------------------------------------------------
> LOEWE Center for Synthetic Microbiology
> AG Bange - Analysis of Metabolic Networks
> Dr. Gert Bange
> Hans-Meerwein-Strasse, C7
> 35043 Marburg, Germany
> office: +49-6421-28-23361
> fax: +49-6421-28-24430
> web: www.synmikro.com/bange
>
>
>
> Am 23.04.2015 um 18:03 schrieb Misbah ud Din Ahmad <misba.ah...@gmail.com>:
>
> > Dear crystallographers,
> >
> > The PDB entry
> > http://www.rcsb.org/pdb/explore.do?structureId=3BDN
> > has 16.5% Ramachandran outliers. When I opened this PDB file in coot and
> > checked for Ramachandran outliers, the results are:
> > In preffered region: 58.04%
> > In allowed regions: 19.78%
> > Outliers: 22.17% !!!!!!!!!
> >
> > With an R-free of 37.4% at 3.9 A resolution, could you please tell me how
> > reliable this structure of Lambda repressor bound to DNA is?
> >
> >
> > Thanks
> > Misbha
> >
> >
> >
> >
> >
> >
> >
>
--
Ethan A Merritt
Biomolecular Structure Center, K-428 Health Sciences Bldg
MS 357742, University of Washington, Seattle 98195-7742
