In the last months we have seen different versions of Refmac give different
maps when displayed in Coot, i.e.
one version giving "nicer" agreement and no difference peaks in some
difficult areas and another version resulting in sharp differences where it
was hard to build the protein. We did not in
Two topics today...
1) Problem with LIBCHECK.
Thanks to all who replied to my issue. I was able to resolve the issue
before the flurry of responses came in. Basically, I took my CSA modified
amino acid, aligned it as best I could to the CYS (especially at the CA),
and then manually edited the PDB
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Hi Petr,
a few things to consider:
1) Fourier truncation ripples:
- CCP4 Newsletter
http://www.ccp4.ac.uk/newsletters/newsletter42/content.html
On the Fourier series truncation peaks at subatomic resolution
Anne Bochow, Alexandre Urzhumtsev
- Pages 52-55 here:
htt
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Hi Debajyoti,
Migration of proteins in SDS containing gels is dependent on hydrophobicity,
the amount of SDS that your protein binds (despite the fact that in theory
all proteins should behave the same way under these conditions) and charge.
Highly basic or acidic proteins will migrate anomalously
Dear All,
Sorry for the off topic question.
I am purifying one protein which is showing increased molecular weight +5kDa
(more than adding up the Hexa His and cloning artifact) in normal 12% SDS PAGE.
The DNA sequence is as it is. The gel runs without blurring the lanes and
without any difficu
Chris,
Crystals can be very tollerant of cryo-solutions that respect the degree
of hydration
of the lattice. You can use any cryo-solution you want, including oil.
Try 10% Di-ethylene glycol, 10% 1.2-propanediol, 10% glycerol, 10% PEG
10K, 10% buffer solution, 1M NaCl
(pH close to the one
Chris,
As others have said, using sugars as cryoprotectants is a good first
choice. However, we have run into problems freezing crystals with
sugars when the primarily crystallization reagent is a salt at high
concentrations (0.8-2M). Although 0.4M ammonium phosphate, is not
particularl
Hi Jacob -
These references might(?) be helpful:
Proteins. 1995 Dec;23(4):580-7. Protein-protein interaction at crystal
contacts. Janin J, Rodier F.
J Mol Biol. 2004 Feb 27;336(4):943-55. A dissection of specific and
non-specific protein-protein interfaces. Bahadur RP, Chakrabarti P, Rodier
F, J
I always try sugars for everything. There is a cryocrystallography webinar
at rigaku.com with embedded videos on how to do this. 50% to 100% saturated
sugar (sucrose, glucose, trehalose, sorbitol, et al.) in reservoir buffer is
usually what I try. :)
-Original Message-
From: CCP4 bulleti
Firstly, I think in Pymol there is no true electrostatic potential
calculator, but only a "charge-smoothed" surface presentation (
http://www.pymolwiki.org/index.php/Protein_contact_potential).
So, If you want to calculate the real electrostatic potential in Pymol (by
Possion-Boltzman method), you
The screen described here might be worth checking out as well:
Crystallization of bFGF-DNA aptamer complexes using a Sparse Matrix designed
for protein-nucleic acid complexes
Jamie J. Cannone, , Cindy L. Barnes, , Aniruddha Achari, and Craig E.
Kundrot ,
Journal of Crystal Growth
Volume 232, Iss
If you are using TLS refinement the please check TLS definitions.It may be that
atoms for which you have positive density are not in TLS definitions.
Try to use without TLS.
regards
Garib
On 26 May 2011, at 11:11, Petr Kolenko wrote:
> Dear colleagues,
>
> I have two problems in two structure
Dear Chris,
Indeed,. according to McFerrin and Snell, 2002, Appl. Crystallogr.,
they recommend 30%(v/v) PEG400, or 35% EG (ethlylene glycol) or 30%
PG (propylene glycol)
However, they also mention the use of 35% (v/v) glycerol.
regards
Kristof
On 26 May 2011, at 13:01, herman.schreu...@sano
regarding the first question - is it now not much more common to refine only
against work reflections, and not do a final refinement agains all reflections?
(avoids the problem rather than solve it, I admit)
regarding the second question - if you take the model from refmac and calculate
a map us
Dear colleagues,
Thanks for the responses. But, Zn occupancy is not an issue. There is
positive maximum, not negative. And Q2, I tried to do it in coot and
also in text editor. Both results were the same. And I double-checked
the line for the atoms in the pdb file for ADP and occupancy.
Regarding
60% occupied Zn site perhaps ?
Q2 do you have leftover atoms from a previous dual conformation refinement ?
Try deleting the corresponding residues in a texteditor and not coot to ensure
they are really gone, then rebuild the section into the new diff- map.
Jürgen
..
Jürgen
Dear Jacob,
I do not have exactly what you are asking about but some clues.
I am not fond of using buried surface area as an indicator of anything in
particular and always use energy estimates, however unreliable they may be. In
J.Comp.Chem. 31(1),133-143, I put a probability plot for PISA to g
How very odd!
I have no ideas on the Zn phenonema - what do the R factor plots look
like against resolution - is there some aberrant reflection which was
part of the FreeR set? The theory is that excluding 5% of the data
should not affect the model seriously at all..
Re the 2nd point. Two
Dear Chris,
I have not used this particular condition, but as a rule of thumb I use
"like with like", e.g. glycerol, ethylene glycol, PEG400 etc. with PEG
conditions, and saltlike compounds (sucrose, xylitol, salts) for salt
conditions. In your case I would try glucose or xylitol or just look
what
Dear Maher,
as far as I know pymol uses the APBS (http://www.poissonboltzmann.org) for the
calculations and your question is answered in the FAQ:
http://www.poissonboltzmann.org/apbs/frequently-asked-questions/what-are-the-units-of-electrostatic-potential
(kT/e)
I don't know if this also answers
Hi,
I would like to get recommendations for a proper cryo solution for a
crystallization hit from the Hampton crystal screen Ammonium di-
hydrogen phosphate 0.4M. I tried increasing glycerol up to 30% with
the same ammonium phosphate concentration or increasing glycerol up to
30% in the pre
Dear colleagues,
I have two problems in two structure refinements using REFMAC5.
1) 1.8A resolution, zinc in the active site. Refinement using work
reflections - ADP for Zinc was about 14. Final refinement including
all reflections increase ADP to 20 or even higher values - followed by
very high
Hi,
Hampton research claims that their Natrix series of screening kits is
designed for nucleid acid and nucleic acid/protein complexes.
http://hamptonresearch.com/product_detail.aspx?cid=1&sid=27&pid=8
Fred.
dengzq1987 wrote:
hello all,
is there any screen kit that is highly effective for
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