Hi,
I'm sure there are proteins that were crystallized at low pH but I can't
remember which. The best thing is to go to the BMCD database:
http://xpdb.nist.gov:8060/BMCD4/index.faces
and query it with the key pH (look into advanced search).
Cheers,
Boaz
Boaz Shaanan, Ph.D.
Tendamistat (1OK0) was crystallized at pH 1.3 and diffracted to 0.93A.
George
On Mon, Nov 07, 2011 at 05:19:29AM +, Sam Arnosti wrote:
Hi everyone
I have a protein that is extraordinarily stable at PH=3.0 or even 2.0.
I want to crystallize it in the low PH and compare the differences
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Something must be wrong..
If you are using REFMAC it will give you a list of bad contacts etc in
the log file..
Check those and try to correct them..
Eleanor
On 11/06/2011 05:04 PM, Zhipu Luo wrote:
Dear all
I have a protein soaked in a coordination compound containing platinum. Due to
I'm not convinced that you need a conventional buffer at pH 2 or 3. At pH 2,
the hydrogen ion concentration is 10 mM. If you want to use something else,
the second pKa for sulfuric acid is around 2. The first pKa for phosphoric
acid is slightly higher than 2. Lactic acid has a pKa close to
I have crystallized in PEG with citrate at pH 3. If you want to go lower
I would suggest maleate:
effective pH range pKa 25°Cbuffer
1.2-2.6 1.97 maleate (pK1)
2.2-6.53.13 citrate (pK1)
Enrico.
On Mon, 07
I remembered that people had crystallize a series of
streptavidin-2-iminobiotin structures at a low pH. If it might help, check
the following PDBIDs:
2RTD
2RTE
2RTI
2RTK
2RTL
Hi everyone
I have a protein that is extraordinarily stable at PH=3.0 or even 2.0.
I want to crystallize it in the
On Mon, 2011-11-07 at 05:19 +, Sam Arnosti wrote:
Hi everyone
I have a protein that is extraordinarily stable at PH=3.0 or even 2.0.
I want to crystallize it in the low PH and compare the differences between
the crystals in regular PH and low PH.
I was wondering how people set up
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Glutaraldehyde works best at low pH
On Mon, Nov 7, 2011 at 8:40 AM, Ed Pozharski epozh...@umaryland.edu wrote:
On Mon, 2011-11-07 at 05:19 +, Sam Arnosti wrote:
Hi everyone
I have a protein that is extraordinarily stable at PH=3.0 or even 2.0.
I want to crystallize it in the low PH and
I would like to see the electron density map (2Fo-FC, Fo-Fc, omit map) for
ligands on 2-fold symmetry in protein structure. If any of you can send some
images I will appreciate it.
Thanks
Debasish
Debasish Chattopadhyay, Ph.D.
University of Alabama at Birmingham
Hi,
I was trying to use SHELXD to solve peptide structure. But I got stuck in
the input .ins file, and I need some advice.
In the .ins file,
TITLE
CELL
ZERR
LATT
SYMM
SFAC C H N O
*UNIT*
*FIND*
*PLOP*
NTRY
HKLF
END
A rough estimate, there will be 62 C, 122 H, 14 N, 32 O in one unit cell.
1 for
The new Phaser GUI does not seem to let me reset the number of clashes
for the packing search?
Is there something I have missed?
Eleanor
Hi,
I was trying to use SHELXD to solve peptide structure. But I got stuck in
the input .ins file, and I need some advice.
In the .ins file,
TITLE
CELL
ZERR
LATT
SYMM
SFAC C H N O
*UNIT*
*FIND*
*PLOP*
NTRY
HKLF
END
A rough estimate, there will be 62 C, 122 H, 14 N, 32 O in one unit cell.
1 for
Hi Eleanor,
I think you should find it in the Additional Parameters section, second line,
labelled Packing criterion. The default (chosen largely because you had been
asking for something like this!) is to allow a number of clashes equal to 5% of
the number of residues.
Let me know if it
UNIT specifies the number of atoms of each type in the unit-cell. For such
'small-molecule' problems you should try to get the numbers of heavier atoms
correct, if only CHNO are present any numbers will do.
For such problems I recommend setting FIND to about 70% of the number of atoms
(excluding
At the risk of sounding like another poll, I have a pragmatic question
for the methods development community:
Hypothetically, assume that there was a website where you could download
the original diffraction images corresponding to any given PDB file,
including early datasets that were from
This is a very good question. I would suggest that both versions
of the old data are useful. If was is being done is simple validation
and regeneration of what was done before, then the lossy compression
should be fine in most instances. However, when what is being
done hinges on the really
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Reluctantly I am going to add my 2 cents to the discussion, with various
aspects in one e-mail.
- It is easy to overlook that our business is to answer
biological/biochemical questions. This is what you (generally) get grants for
to do (showing that these questions are of critical importance
So far, all I really have is a proof of concept compression algorithm here:
http://bl831.als.lbl.gov/~jamesh/lossy_compression/
Not exactly portable since you need ffmpeg and the x264 libraries
set up properly. The latter seems to be constantly changing things
and breaking the former, so I'm not
Dear James,
You are _not_ wasting your time. Even if the lossy compression ends
up only being used to stage preliminary images forward on the net while
full images slowly work their way forward, having such a compression
that preserves the crystallography in the image will be an important
I'll second that... can't remember anybody on the barricades about
corrected CCD images, but they've been just so much more practical.
Different kind of problem, I know, but equivalent situation: the people
to ask are not the purists, but the ones struggling with the huge
volumes of data.
Dear ccp4bbers,
I wonder if someone can help me defining proper weight matrix term in
Refmac5 to lower the R-FreeR gap. The log file indicates weight matrix of
1.98 with a gap of 7. Thanks for suggestions in advance.
James
So the purists of speed seem to be more relevant than the purists of images.
We complain all the time about how many errors we have out there in our
experiments that we seemingly cannot account for. Yet, would we add
another source?
Sorry if I'm missing something serious here, but I cannot
I think that real universal image depositions will not take off without a
newish type of compression that will speed up and ease up things.
Therefore the compression discussion is highly relevant - I would even
suggest to go to mathematicians and software engineers to provide
a highly efficient
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