The geometry targets for protein are well established (by which I mean
"agreed upon") and so the distribution
On 18/03/2021 07:19, Cyril Hamiaux wrote:
Dear Jasmine (and all),
Many thanks for the article. I have a question regarding the Z cutoffs
used to flag geometry outliers in the PDB validation reports: geometry
outliers are flagged with |Z|>2 for ligands (including carbohydrates),
but with |Z|>5 for proteins. What is the rational for using different
criteria for ligands vs proteins? After all isn’t this just one structure?
The geometry targets for protein are well established (by which I mean
"agreed upon") and so we can presume that the distribution for
refinement is similar to that of the validation. One cannot say as much
for ligands at the moment. the wwPDB wants to flag only what they have
confidence are wrong. In the CCP4 world, yes, it's all homogeneous (or
that is the intent (carbohydrates in particular need some attention in
the monomer library (I'd recommend that you just run Acedrg to update
the dictionaries (or use Coot, where this have been done for you))), but
the wwPDB doesn't score with CCP4 software (not today at least).
PS. I am refining a 2.4 A resolution structure of a N-glycosylated
protein and end up with a large number of geometry outliers for the
sugars when I generate PDB validation reports (especially angle outliers).
Are you using/did you use the N-linked glycan builder in Coot? because
this really shouldn't happen if you are (it uses modern Acedrg-based
dictionaries). If not, you can still use "Refine Tree" and it should
(might?) do something helpful.
The huge majority of these outliers are flagged with |Z|<5 (ie they
would not be flagged if they were protein bonds or angles). The
electron density for the sugars is quite good and I made sure that
correct LINKR records are used during refinement in Refmac. I must
admit that I’m a bit struggling to improve this.
Refmac can report distance deviations, so you can see where the
restraints are fighting the density.
You can do something similar in Coot too.
Paul.
*From:*CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> *On Behalf Of
*Jasmine Young
*Sent:* Thursday, 18 March 2021 2:46 am
*To:* CCP4BB@JISCMAIL.AC.UK
*Subject:* [ccp4bb] Enhanced Validation of Small-Molecule Ligands and
Carbohydrates
A new article in
/Structure/<https://doi.org/10.1016/j.str.2021.02.004>describes new
features, including branched representations and 2D SNFG images for
carbohydrates, identification of ligands of interest, 3D views of
electron density fit, and 2D images of small molecule geometry.
These enhancements and processes for validation of 3D small-molecular
structures reflect recommendations from the wwPDB/CCDC/D3R Ligand
Validation Workshop and the adoption of software through community
collaborations.
This manuscript also highlights enhancements made since the initial
implementation of Validation Reports as described in Validation of the
Structures in the Protein Data Bank (2017) Structure 25: 1916-1927
doi: 10.1016/j.str.2017.10.009<https://doi.org/10.1016/j.str.2017.10.009>.
*Enhanced Validation of Small-Molecule Ligands and Carbohydrates in
the Protein Data Bank *
Zukang Feng, John D. Westbrook, Raul Sala, Oliver S. Smart, Gérard
Bricogne, Masaaki Matsubara, Issaku Yamada, Shinichiro Tsuchiya,
Kiyoko F. Aoki-Kinoshita, Jeffrey C. Hoch, Genji Kurisu, Sameer
Velankar, Stephen K. Burley, and Jasmine Y. Young
(2021) Structure doi:
10.1016/j.str.2021.02.004<https://doi.org/10.1016/j.str.2021.02.004>
undefined<https://doi.org/10.1016/j.str.2021.02.004>
<http://www.wwpdb.org/news/news?year=2021#top>
--
Regards,
Jasmine
===========================================================
Jasmine Young, Ph.D.
Biocuration Team Lead
RCSB Protein Data Bank
Research Professor
Institute for Quantitative Biomedicine
Rutgers, The State University of New Jersey
174 Frelinghuysen Rd
Piscataway, NJ 08854-8087
Email: jasm...@rcsb.rutgers.edu <mailto:jasm...@rcsb.rutgers.edu>
Phone: (848)445-0103 ext 4920
Fax: (732)445-4320
===========================================================
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