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%
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.
Best and god save the EDS,
Gert
-
LOEWE Center for Synthetic Microbiology
It was published in Nature so it must be right :) ...
Dear crystallographers,
The PDB entry
http://www.rcsb.org/pdb/explore.do?structureId=3BDNhttp://www.rcsb.org/pdb/explore.do?structureId=3BDN
has 16.5% Ramachandran outliers. When I opened this PDB file in coot
and checked for
Dear Gert,
I just did that and I wonder how these structures end there !!!
@ Sabine: I was talking about Ramachandran outliers. I had learnt that the
number of Ramachandran outliers show be very few or none for low resolution
structures.
On Thu, Apr 23, 2015 at 6:25 PM, Gert Bange
They have, it is call PDB_REDO. You can download the maps and refined structure
there.
http://www.cmbi.ru.nl/pdb_redo/
Dan
Its not just the Ramachandran outliers - the attached metrics summary
courtesy of the PDB raises a lot of questions about the accuracy of
this structure
As for Nature being right, it was an attempt at humor.
Dear crystallographers,
The PDB entry
Is it in pdb redo? Take a look here:
http://www.cmbi.ru.nl/pdb_redo/bd/3bdn/index.html
JPK
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Misbah ud
Din Ahmad
Sent: Thursday, April 23, 2015 2:28 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] 3BDN, 16.5% Ramachandran
My guess is they had the best data they could get, did molecular replacement
with the two halves of the repressor and the dna, got a solution and didn't use
appropriate restraints in the refinement. Like Phoebe mentioned, we have better
tools for this these days.
Dear Misbha,
Before you throw stones at other peoples' work:
- have YOU tried to refine a structure at 3.9A, particularly with older
software?
- there are many structures in the database that are related to lambda
repressor. Have you checked how the structure in question compares to those
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
The abstract of the papers says they used MIR.
Mark J van Raaij
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia - CSIC
c/Darwin 3
E-28049 Madrid, Spain
tel. (+34) 91 585 4616
http://www.cnb.csic.es/~mjvanraaij
On 23 Apr 2015, at 18:57, Todd Jason Green wrote:
The methods part of the 2008 nature paper also mentioned the two earlier,
high-res structures 1F39 (1.9 A) and 1LMB (1.8 A), which together cover
almost the whole strucutre except the linker regions.
I wonder, in such situations, is it a good practise to use the high res
structures, either as
Dear Phoebe A. Rice,
I didn't mean to discredit the work but the statistics of the structure
just shocked me at the first instance.
I could for example point out to another structure 1ZR2, which has the same
resolution (the protein Molecular weight is almost the same) and the
statistics are:
Isn't the only criteria for EDS that calculated R (by EDS) is +/- 5% of
reported R?
On Thu, Apr 23, 2015 at 12:35 PM, Misbah ud Din Ahmad misba.ah...@gmail.com
wrote:
Dear Gert,
I just did that and I wonder how these structures end there !!!
@ Sabine: I was talking about Ramachandran
Elaborating on Phoebe's answer, the question to ask is : is the structure good
enough to support the conclusions reached in the paper ?
That is, quoting the abstract : an unusual overall architecture that allows it
to adopt a conformation that appears to facilitate pairwise cooperative binding
The abstract of the papers says they used MIR.
Mark J van Raaij
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia - CSIC
c/Darwin 3
E-28049 Madrid, Spain
tel. (+34) 91 585 4616
http://www.cnb.csic.es/~mjvanraaij
On 23 Apr 2015, at 18:57, Todd Jason Green wrote:
My
At around 4.0 A resolution one normally cannot talk about accuracy. The
density will at most locations not warrant any detailed interpretation.
If, at 4.0 A resolution, you move atoms around a bit, you will not see
significant changes in R/Rfree. So, you can do whatever you want, more
or less.
Hi,
I entirely agree with Phoebe. This is 2008 structure (publish date, so
refinement was probably done in 2007) - that is before all the new methods
and tools for low-res refinement became available.
Now, let's have a closer look... Given rather large amount of various
geometry outliers (in
I feel rather uncomfortable and cornered with the aggressive replies and
phrases like throwing stones, public humiliation etc., which suggest
that I have some personal enmity with the author. The structure is in the
public domain and questions can be asked about it. I as a beginner in
Well, with full respect to your sensitivities as far as your own person is
concerned: if you play rough (and 5 exclamation marks qualify by commonly
accepted email etiquette as incipient flame, at least), you need to be willing
to take a few as well...
Best, BR
How reliable is too general a question - it depends on what you want to know.
At 3.9Å they could probably place the phosphate atoms quite well and see the
general fold of the protein.
Finer details will be less reliable, i.e. where the exact side-chains are etc.
They could probably have forced
Hi Hans,
I would get in touch with folks from Art Robbins
(http://www.artrobbins.com/hydra-service/). They may be able to help you.
Good luck,
Gopal
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
Brandstetter Johann
Sent: Thursday, April 23, 2015 8:25 AM
Dear colleagues,
we have problems to find a replacement for the protein nano-dispenser (needle)
of our Hydra II crystallization robot which was previously distributed by the
company Matrix, later taken over by Innovadyne, then by Thermo Fisher (who do
no longer support the system).
For
Dear Mintu,
If I understand your scenario correctly, you are referring to a single
structure where you want to get the relative inter-domain orientation
within the one protein.
So, after having watched the Chimera tutorial movie linked in the
previous answer (just out of curiosity) and then
Hi,
In my experience, additive screens (e.g Hampton's) can change crystal
morphology. You could also re-screen for new conditions either using matrix
micro seeding, or change the protein buffer. Perhaps adding a ligand or a
component from your current crystallisation conditions to your protein
Dear Colleagues,
The ARC Centre of Excellence in Advanced Molecular Imaging is seeking to
appoint a computational Senior Research Officer (Computation) to help boost our
efforts in developing the automation systems of the MX beamlines at the
Australian Synchrotron utilising the Multi-modal
Dear All,
This is more a biochemical/biophysics question but since we need to
complete our structural analysis with functional or biophysical data, I
thought I would ask. We crystallized a protein as an MBP fusion and solved
its structure. Based on previous knowledge we know that the small
I have not seen this with mbp before, however you could try fret instead...
Artem
On Apr 23, 2015 9:26 PM, Pascal Egea pas...@msg.ucsf.edu wrote:
Dear All,
This is more a biochemical/biophysics question but since we need to
complete our structural analysis with functional or biophysical
Hi Pascal,
Can you give us some details about your experimental setup?
If I had to guess, are you using monochrometers set to approximately 2x Trp
EX/EM. You may be able to solve this by just adding some cheap colored glass
high pass filters to the optical path.
Shae Padrick
On Apr 23,
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