I agree that density looks dubious, the B-factor distribution among DNA atoms is odd (sudden shifts from blue to red) and the little wwPDB bar charts are on the red side.
But what about the density for the protein?
The structure is of a hexameric helicase with with dsDNA going through the hole, so the space group being nearly-R3 or R32 doesn't shock me: one would expect the DNA to subtly break the symmetry.
Could it simply be very poorly ordered DNA going making a pseudo-continuous helix going through the crystal? Or maybe the symmetry isn't broken, and DNA backbone is in 3 different rotational states even if there's rough density for the planes of the bases?
++++++++++++++++++++++++++++++++++++++++++
Phoebe A. Rice
Dept. of Biochemistry & Molecular Biology
The University of Chicago
[log in to unmask]
https://voices.uchicago.edu/phoebericelab/
________________________________________
From: CCP4 bulletin board [[log in to unmask]] on behalf of Anastassis Perrakis [[log in to unmask]]
Sent: Thursday, November 30, 2017 12:56 PM
To: [log in to unmask]
Subject: Re: [ccp4bb] Electron density in PDBe
Interesting structure:
a=b=c=á=â=ã=107 in P1
Estimated twinning fraction 0.439 for k,l,h and 0.439 for l,h,k
In other words R32? ;-)
The PDB-REDO map has some interesting features, one strand has bases density at .0 sigma, the other not, see attched.
The NCS averaging they used is kind of interesting. It reads correct if I read through, but if something is done wrong, I am guessing it might result in erronous features.
As a side note, the refereeing in eLife is interesting. The reviewing editor is Stephen Bell; an excellent scientist, but not a crystallographer. Referees opted to stay anonymous - but one could speculate they are not crystallogrpahers either, as they did not raise any crystallographic questions. The validation summary, well, it could have raised some red flags … sorry, it did raise red flags, or to be exact red bold boxes. Evidently, nobody looked at them.
Have fun -
A.
[cid:B25D7E2E-FD64-40A6-9DBD-60DEF50D9249@home]
[cid:5B0AA6A0-834B-46C7-AE56-8C6DFFB2F62D@home]
A.
On 30 Nov 2017, at 19:01, Wim Burmeister <[log in to unmask]<mailto:[log in to unmask]>> wrote:
Dear all,
I am doing some analysis on pdb entry 5tct.
I realized that the electron density on the PDBe site (obtained from EDS) shows much more model bias than the one obtained from the pdb file and the cif reflection data file using ccp4i (import + refmac5 with 0 cycle positional refinement). Using the mtz file from pdb-redo a similar map is obtained.
When I read the publication 5kleywegt et al, 2004) on EDS, I understood that essentially the same approach is used (refmac with 0 cycle refinement followed by fft map calculation).
Does anybody have an idea where the discrepancy comes from ?
I join a jpg with the electron density of the 3 approaches. The contour level is about 3 sigma.
Best,
Wim
ps: I expect that the electron density of the DNA is not really present as the entry has a number of flaws.
--
Wim Burmeister
Professeur
Institut de Biologie Structurale (IBS) CIBB
71 avenue des Martyrs
CS 20192
38044 Grenoble Cedex 9, FRANCE
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website<http://www.ibs.fr/research/research-groups/viral-replication-machines-group-m-jamin/team-03/article/poxvirus-replication-machinery-presentation/>
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