Dear all,
I am dealing with a protein/DNA complex. After restrained refinement
in Refmac, the bases have been brought closer to each other (about 2A
instead of 3A for H-bonding). But in our model, the geometry of the DNA is
fine (I even replaced my DNA with theirs by superimposing and edi
Hi Jose Antonio Cuesta Seijo,
- at 3.1A I would try 1) refining individual isotropic ADPs, 2) combined
strategy of refining TLS+individual isotropic ADPs, 3) combined strategy
of refining TLS+group isotropic ADPs with one or two definable isotropic
B-factor per residue. Look at Rfree and Rfree
> If all cells are completely unsynchronized, then the
occupancy-weighted
> average electron density map of all the conformers will fully explain
> the background-subtracted spot intensities, but if there is
> cell-to-cell synchronization: it won't!
This is not correct: as I tried to explain in
On Thursday 28 January 2010 09:57:31 John Badger wrote:
> Hi Ethan,
> Your effort to play devils advocate is appreciated - I have not seen much
> debate on the applicability of TLS so at risk of diverging into a separate
> thread:
>
> I would not argue that TLS is necessarily a valid model for c
John Badger wrote:
Diffuse scatter patterns were compared to simulations of correlated motions
that were long-range (say, the size of the whole molecule) ...
This is exactly not the point I was trying to make. Anything confined
to a single unit cell is not what I would call "long range".
Hello,
1. The reduction in number of parameters is not that significant. On
average, you have some 8 atoms per residue, and thus 32 parameters with
individual B-factors (4 per atom). With grouped B-factors you have 26,
about 20% difference. While it sounds like a lot (hey, I just removed
2000
Hi Ethan,
Your effort to play devils advocate is appreciated - I have not seen much
debate on the applicability of TLS so at risk of diverging into a separate
thread:
I would not argue that TLS is necessarily a valid model for correlated motion
in
proteins because it 'works' in fitting the ava
NEB recommends adding Zn for Antarctic Phosphatase. Although we found it
works in all NEB restriction enzyme buffers.
The answer can be found at
http://www.neb.com/nebecomm/products/faqproductM0289.asp.
--Chun
_
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf
Look into AKRAprime. It's good for low pressure columns (Max 1MPa) and costs
~$14,000 with accessories. For the price of a FPLC, we have several
AKTAprime for running SEC columns. --Chun
_
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of
Sangeetha Vedula
Sent: Thur
Dear Nenci
I always used CIP with great success. A good control to test whether CIP
worked, a plate with a plasmid (containing no insert) should not ligate and
will not be circular, hence if CIP worked, this plate should not contain any
plasmids grown on it (or very few).
However, if you were to
This is the basis of the TAILS "correction" in Scala, but I'm not convinced it
works very well, particularly if you don't have lots of fully recorded
reflections
Phil
On 28 Jan 2010, at 15:41, Dirk Kostrewa wrote:
> Dear James,
>
> Am 27.01.10 10:08, schrieb James Holton:
>
>> I'm still no
We've been using Bio-Rad biologic duoflow FPLCs for over 5 years (we have 4
of them on site). They can also handle abuse and cold room storage. Their
hardware and software are user-friendly. It seems the Profinia system is
geared toward simpler purifications.
You really don't need much of a system to do just
affinity purification, so almost anything would be workable unless you
are doing really high throughput work. On the other hand, if you need
to do traditional protein purification (IEX, HIC, GEC), which would
include untagged proteins, and polis
You know what, decarboxylation could be an issue. But that'll explain the
B-factors only for the side chains and some of the atoms in the ligand.
I don't see in what other orientation/conformation the ligand can fit the
density, not clash with itself or with the protein, lie on a 2-fold symmetry
a
Thanks for your response, Edward. Yes, that is what I thought. For the most
part, people plan to tag their proteins in my lab. I'll possibly be the only
one purifying non-tagged proteins in my lab. I love the AKTA. Another was
all praise of the Profinia. To my knowledge, tagged proteins don't alway
Dear Sangeetha,
before worrying about the B-factor column in your PDB file I would be
worrying about atoms not having density. This should tell you that
your model (atoms and/or parametrisation) isn't correct.
One possible reason for those high-B side-chain atoms could be a
sequence shift: someti
On 24/01/10 23:11, Matt Harrington wrote:
> Hi Justin,
>
> Did you receive a response to this? Would you mind if I reposted your
> question to http://www.BioKlatch.com? It's an online forum for
> structural biology that I'm starting. I haven't announced it yet and
> am pre-seeding it with quest
Dear all,
My lab is looking into buying a protein purification system. The AKTA is
more versatile, but does anyone know if the Profinia is in any way superior
to the AKTA for purification of affinity-tagged proteins? If it is, I would
really appreciate if you can tell me in what way it is superior
Dear all,
I am refining a crystal structure with two enantiomers of the ligand lying
on a two-fold crystallographic axis (making the density an average of 4
orientations/optical identity). The ligand fits pretty well over all in the
density, but some atoms stick out of density. While B-factors for
Dear James,
Am 27.01.10 10:08, schrieb James Holton:
I'm still not really sure what the difference is between a Bragg spot
and a feature "under" it. Why not define a "Bragg intensity"
operationally? Subtracting local background with a least-squares
plane is pretty much universally done, and
Dear CCP4BB-ers,
The official DSSP is now also available for Intel Macs:
http://swift.cmbi.ru.nl/gv/dssp/
We have limited access to Mac computers, so the software is not as thoroughly
tested as the Linux and Windows versions. Feel free to send bug reports.
Best wishes,
Gert Vriend & Robbie
I need to dephosphorilate blunt ends and, surfing on internet I found this
two enzymes:
- Shrimp Alkaline Phosphatase (SAP)
- Calf Intestinal Alkaline Phosphatase (CIP)
Have you any experience about these phosphatases, I mean wich is the best
for blunt ends?
Either will do dephosphorylation p
Jose Antonio,
I've seen similar behavior few years ago with grouped B-factor
refinement in CNS. The argument for the grouped refinement is as
follows:
This is better than individual B-factor refinement at low resolution
because you significantly reduce the number of parameters.
There are two h
Hi Mark.
This is hidden in the "Extensions" menu.
Extenstions -> Maps-> Transform map by LSQ model fit
Or at least that is what I think you want.
Best regards,
Folmer Fredslund
On 28 January 2010 15:29, Matt Warkentin wrote:
> Hi all
>
> I have a seemingly simple task that I can't seem to fig
Hi all
I have a seemingly simple task that I can't seem to figure out how to
do: I have a bunch of structures with same space/cell that I want to
compare in coot. It is easy to superpose the models, but I would also
like to superpose the maps. Is there a simple way to do this? If
not, is that
I need to dephosphorilate blunt ends and, surfing on internet I found this
two enzymes:
- Shrimp Alkaline Phosphatase (SAP)
- Calf Intestinal Alkaline Phosphatase (CIP)
Have you any experience about these phosphatases, I mean wich is the best
for blunt ends?
All the best
Nenci Simone
--
Research Associate in Structural Biochemistry
Limit of tenure: up to 31st August 2013. Salary: £27,319-£35,646 per annum
A postdoctoral position is available in the Department of Biochemistry of the
University of Cambridge, UK to study structure and function of macromolecular
complexes importan
John, Ethan
Some good points being made regarding the discrepancy between TLS models
and measured diffuse scatter. However, as James has pointed out,
measuring the diffuse scatter is not that easy due to the contribution
of the lattice This could be why there are some problems as large
motions (d
Dear all,
I am refining a 3.1Å structure with Phenix.refine, using two ADP groups per
residue.
When doing refinement in Refmac, the way to go would be to tighten the
weights quite a bit to make up for the low resolution, resulting in small
deviations in bond lenghts and angles from the ideal value
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