I like cases like this as cautionary tails for the crystallography class. In
this case, the sequence is mismatch in several places, ex. residues 1165-1170
should be 1153-1158 which flows nicely after you add a residue to 1151. There
are other places where the mainchain has slid and is out of reg
I don’t think anyone mentioned contacting the authors first—doesn’t this seem
like the first thing one should do?
Jacob
+
Jacob Pearson Keller
Research Scientist / Looger Lab
HHMI Janelia Research Campus
19700 Helix Dr, Ashburn, VA 20147
Desk: (571
If it is as it appears, it is disappointing to see this in JACS. I would
expect better. Unfortunately, reviewers don't always get a lot of
information to judge quality of structures (which has been discussed
extensively on prior occasions on this board), so some trust is
involved that what dat
Even though PDB-REDO cannot salvage this model without extensive rebuilding
which is what Tristan showed, it is fun to look at the maps and B-factors near
the ligand. The B-factors go way up and the negative difference density
disappears, as does most of the 2mFo-DFc density. It’s obviously not
Begin forwarded message:
From: "charles w carter, jr" mailto:cwcar...@ad.unc.edu>>
Subject: Re: [ccp4bb] Questionable Ligand Density: 6MO0, 6MO1, 6MO2
Date: July 19, 2019 at 1:32:53 PM EDT
To: Patrick Loll mailto:pjl...@gmail.com>>
Hi Pat,
I, too have fallen into this rabbit hole while Mark Ro
Would it be possible to add a public annotations section to the PDB, to allow
us to potentially flag/warn whoever downloads that particular structure, there
could be something wrong with it, such as wrong space group, no/poor density
fitting for ligand. Something similar to PubPeer maybe?
Dani
The idea of contacting the editor (and/or author) is an excellent one, and
indeed the correct thing to do scientifically. However, I’m disillusioned: I’ve
been down this path before with a high-profile vanity journal, and while the
editors paid lip service to the notion that the record should be
Hi Tristan et al,
before people invest their time into re-refining a model against the deposited
data, I'd suggest that these data are dubious - see table S3 in
https://pubs.acs.org/doi/suppl/10.1021/jacs.9b02505/suppl_file/ja9b02505_si_001.pdf
! The data processing statistics look "surprising"
I couldn't resist doing a little playing with 6mo0 in ISOLDE. The
sequence past Gly1151 is wrong - after jumping a small gap (density
clearly indicates a single missing residue here), it continues on from
1165. Corrected the following sequence to GVVTRS, deleted the ligands,
did some basic ener
Hi Rhys,
the reported B-factors for the “ligands” are all way below the reported
B-factors for the protein chains, with the worst of the three complexes
reporting unitless numbers 23.2 and 64.8, respectively, just to highlight *one*
striking feature of the data collection and refinement table.
Hi Rhys,
all three structures are at modest resolution and they don't seem to
be properly refined. At least they are all below average. I wonder
how this paper made it past the referees.
I haven't checked the paper, but there are ways and means how to
deal with weakly bound ligands in the best p
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The validation reports are pretty bad, so it seems to be a case where the
referees and editor have not checked them.
And, like Herman wrote, the models do not appear to agree well enough with the
maps - in all three cases.
Mark J van Raaij
Dpto de Estructura de Macromoleculas
Centro Nacional de
Hi Rhys,
There is definitively some density present for a ligand, but the active site
region looks completely misfitted, and the ligand density may also belong to
unfitted protein residues. One first needs to get the protein chain right, and
should then look if there would still be density avai
Hi All,
I was chatting with a colleague during a recent synchrotron visit and
they'd recently come across some ligand/drug bound structures associated
with a paper recently published in a high impact factor journal.
They had pulled the associated SFs from the PDB and found that the electron
densi
Dear All,
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Dear Mario,
you probably want to run more than NTRY 1000. With today's computers, NTRY
5000 or NTRY 1 should not take very long.
You high resolution cut-off in shelxd, 2.7A, is the default, as shelxc adds
0.5A to the high resolution limit of the full data set. In your case this
seems reaso
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