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Dear All
I want to search SUMO interacting motif (SIM) in different protein data bases
and also in the given protein sequences.
Does anyone can provide me the PROSITE AC and/or ID for the
SIM motif? I will be grateful if you
provide me MATRIX for the SIM motif profile.
I do not know much about h
Hi Arpita
You can try QUANTI-iT
Protein assay kit from Invitrogen.
But still there is
nearly 20-50% discrepancy between this method and a Abosorbance at 280.
I also faced same
problem with a protein, then re-cloned by adding a Trp at the C-terminus.
Raj
E. Rajakumara
Postdoctoral Fellow Str
Dear All
I have two structures of homo-dimeric protein complex with different DNA.
I want to calculate RMS deviation between second monomer from these two
complexes by fixing superposed first monomer.
This I require to know what is the effect of DNA on relative orientation of two
monomers in the
Dear All
Please can you tell me what is the Cryoprotective ability of low molecular
weight (400kDa) poly-gamma-glutamic acid (LM-PGA) polymer.
If it is cryoprotective then can anybody mail me the percentage of glycerol/EG
addition for the given percentage of LM-PGA.
Thanking you
raj
E. Rajakuma
Dear All
I am Rajkumar, working on the protein which has unusual behavior while
concentration.
When I kept protein in 15 mM Tris 7.5, 150 mM NaCl and 5 mM DTT, the solubility
of the protein is decreases drastically and tend to crystallize while
concentration.
Protein cannot be concentrated mor
t; remove SCALE lines from the pdb and try again. If it
> does not help
> then could you please send me your pdb file and I
> will try to sort out.
>
> Garib
>
> On 16 Mar 2009, at 22:43, E rajakumar wrote:
>
> > Dear All
> > I am refining proitein-DNA comple
d you please
> remove SCALE lines from the pdb and try again. If it
> does not help
> then could you please send me your pdb file and I
> will try to sort out.
>
> Garib
>
> On 16 Mar 2009, at 22:43, E rajakumar wrote:
>
> > Dear All
> > I am refining pro
Dear All
I am refining proitein-DNA complex structure in
Refamac5. When I used coordinate file containing 2
bases less, then the refinement is running smoth and
perfect. But when I built 2 exta bases to the existing
DNA in the coot then refinement is failed with the
following error message.
/usr/
Dear All
I am working on protein-DNA complex crystals for data
collection. These crystals are grown in 15-20 % of
PEG3350 or PEG4000 with pH of 6 to 7. When I soak the
crystals more than a minute in the cryo solution
(15-20% of Glycerol or ethylenglycol + reservoir) the
resolution of diffraction is
Dear All
Sorry for non-crystallography query. I am working on
DNA binding protein, while mixing DNA with protein for
preparing Protein-DNA complex for crystallization,
protein is precipitating. pI of the protein is 9.3
and in 15 mM HEPES 7.0, 150mM NaCl and 5% glycerol.
Concentration of the protei
Dear All
I want to create a random crystallization screen using
given set of crystallization parameters (pH,
Precipitant, salt, additive.) for protein-DNA
complex crystallization. I was using Brent Segelke's
CRYSTOOL program, not accessible online now. Please
can you suggest any other such prog
Dear All
Sorry for non crystallographic query.
Can any body mail me how to prepare Ammonium citrate
tribasic (citric acid triammonium salt) buffer pH 6.7
to 7.25 and also what is the pKa value.
Thanking you in advance
Rajakumara
E. Rajakumara
Postdoctoral Fellow
Strcutural Biology Program
of monovalent
> salt first, not
> just deionized water.
>
>
> On Jun 22, 2008, at 9:10 AM, E rajakumar wrote:
>
> > Hi Artem Evdokimov
> > Thank you for the mail. I have synthesized DMT-on
> > oligos in our laboratory. Deprotection was
> performed
>
clean metal spatula -
> does it burn or does it just sit there (and what
> color does it become).
>
> Normally you can prepare DNA-protein complexes in a
> variety of ways,
> including direct addition, concentration,
> counterdialysis, etc.
> Regards,
>
> Artem
>
Dear All
Sorry for non-crystallography question. I have
synthesized two complementary strands of 16 bases in
length for making duplex DNA and co-crystallization
with DNA binding protein. I have mixed two
complementary strands of 1:1 molar ratio (0.5 mM) in
water and concentrated to 1.5 mM (Duplex),
Dear All
Sorry for non-crystallography question. I have
synthesized two complementary strands of 16 bases in
length for making duplex DNA and co-crystallization
with DNA binding protein. I have mixed two
complementary strands of 1:1 molar ratio (0.5 mM) in
water and concentrated to 1.5 mM (Duplex),
Dear CCP4 users
Sorry for non CCP4 topic.
I want to know a company which can synthesize 5-methyl
2-deoxy Cytidine modified DNA duplex.
Thank you in advance
Rajakumara
E. Rajakumara
Postdoctoral Fellow
Strcutural Biology Program
Memorial Sloan-Kettering Cancer Center
New York-10021
NY
0
Dear All
Sorry for non-crystallography question. I am purifying
a protein using GST column. The gel filtration
chromatography is indicating that the protein is
aggregating at pH more than 7.0. I am planning to
purify the protein at the pH around 6.0. So, I want to
know the affinity of GST-fusion pr
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