Dear experts,
This is a messy question concerning a messy dataset and I try to put it
correctly.
I have a severely anisotropic dataset up to 2.3A that merges quite fine in
all 4/mmm. Automatic indexing is primitive tetragonal but I can push it to
a centered tetragonal cell if I want to. The cryst
Dear Daniel,
A very good question. I have seen R_d plots jumping up and down, most often in
low-symmetry space groups. I think the "mountains" are due to residual
systematic differences between symmetry-related observations, differences that
the scaling could not compensate for whatever reason.
Thanks to all of those that sent in their comments.
For those that have an interest in the consensus (after ~24 hours):
For question one about the PDB deposition code- out of 10: 3 said in footnote,
2 said they had either seen or had put the deposition code in the materials and
methods, and a maj
Postdoctoral position, Columbia University Medical Center, NYC
Postdoctoral position is available in the lab of Alexander Sobolevsky at
Columbia University, Department of Biochemistry and Molecular Biophysics (
http://www.cumc.columbia.edu/dept/gsas/biochem/faculty/ALEXANDERSOBOLEVSKY.htm
).
The
Hi Lucas,
this book (
http://www.amazon.com/Structural-Bioinformatics-Methods-Biochemical-Analysis/dp/0471201995/ref=sr_1_2?s=books&ie=UTF8&qid=1382044405&sr=1-2&keywords=structural+bioinformatics)
brings nice examples of protein structures with "unusual features" in the
structure validation chapt
Yikes! This cuts close to my area. We occasionally have undergrads solve
and refine carbonic anhydrase-sulfonamide structures as a part of a
4-hour biochemistry teaching lab. (We have a whole shelf-full of
sulfonamides that make excellent teaching projects.)
I use 2QNS for teaching. It is an egregious case of modeling ligand into noise.
Also, the structure has many close contacts (e.g. HOH A351), poor
stereochemistry (e.g. A58-A61), and incorrectly built water. Turn on symmetry
to see the steric clash of the peptide ligand with itself. You can g
I would start with 1E4M (residue 361 of chain M) and 1QW9 (170 of
chain B). First show the model and then reveal the electron density.
This promotes a healthy skepticism of PDB models and enforces the
importance of always looking at a model in the context of the map.
For model building I wo
On Thursday, 17 October, 2013 10:51:08 Lucas wrote:
> Dear all,
>
> I've been lecturing in a structural bioinformatics course where graduate
> students (always consisting of people without crystallography background to
> that point) are expected to understand the basics on how x-ray structures
> a
Dear all,
I am using xds (with graphical interface xdsgui) to process several
diffraction data of a membrane protein that I have crystallized. At the
end, I run XDSSTAT in order to check the statistic parameters of the
process and my attention is captured by the R_d plot: R_d drops during
the
From the original ABC transporter retraction:
http://www.sciencemag.org/content/314/5807/1875.2.full
"The Protein Data Bank (PDB) files 1JSQ, 1PF4, and 1Z2R for MsbA and
1S7B and 2F2M for EmrE have been moved to the archive of obsolete PDB
entries"
You can get your hands on them via URLs like
On Thu, Oct 17, 2013 at 6:51 AM, Lucas wrote:
> I wonder if there's a list of problematic structures somewhere that I
> could use for that practice? Apart from a few ones I'm aware of because of
> (bad) publicity, what I usually do is an advanced search on PDB for entries
> with poor resolution a
Sorry, it is acta cryst F69, not 96!
Herman
Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von
Schreuder, Herman R&D/DE
Gesendet: Donnerstag, 17. Oktober 2013 16:11
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [ccp4bb] AW: [ccp4bb] Problematic PDBs
Dear Lucas,
I recently came accross
Dear Lucas,
I recently came accross a scientific comment on the 1.9 Å PDB structure 4i8e,
where apparently a HEPES molecule had been misinterpreted as a disaccharide.
See Ives Muller, acta cryst F96, 2013:1071-1076.
Best regards,
Herman
Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK
Dear all,
I've been lecturing in a structural bioinformatics course where graduate
students (always consisting of people without crystallography background to
that point) are expected to understand the basics on how x-ray structures
are obtained, so that they know what they are using in their bioi
Please see announcement below that can also be seen at
http://www.ku.dk/english/available_positions/vip/ as "Post doctoral
position/assistant professor" with application deadline November 1. If you wish
to apply, you will need to use the link above to the electronic application
system.
All the
Hi,
NUCPLOT is good.
You could also try:
http://utdallas.edu/~hnam/software.php#NuProPlot
Sid
Dr K S Sidhu
Department of Biochemistry
1/61 Henry Wellcome Building
Lancaster Road
Leicester
LE1 9HN
Tel: 0116 229 7237
On 16 Oct 2013, at 20:35, Ni
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