Shankar,
I would suggest to also set up a few plates with your protein in HEPES
instead of Tris. I once worked for months trying to improve tiny crystals
while my protein was in Tris, pH 7.4, to no avail. I got beautiful
crystals when I purified my protein in HEPES, pH 7.4, with everything else
If we are to strictly adhere to polymer as describing "few", then were do
we stand with DNA/RNA being described as a polymer - a long polymer made up
from repeating units of nucleotides, as has been used in textbooks for
ages?! Is DNA/RNA too now a myriomer?
Cale
P.S. I haven't personally tried concentrating with PEG 20K but I suppose
it could work.
On Sat, Jan 28, 2012 at 12:41 PM, Cale Dakwar wrote:
>
> Hello Rashmi,
>
> How large are your protein monomer units? Are you expecting these units
> to have formed an oligomer?
Hello Rashmi,
How large are your protein monomer units? Are you expecting these units to
have formed an oligomer? As a general rule of thumb, you want your protein
molecules to be no smaller than 3x the membrane MWCO. Perhaps all you need
is to try concentrating with a lower MWCO membrane, e.g.
In theory, no: sub-angstrom resolution can be obtained for any and all
proteins, including membrane proteins, and for large complexes. In
reality, it becomes technically very difficult to achieve; you would need
ever-colder temperatures and ever-stronger irradiation sources.
P.S. In theory, the
Hello Lisa,
Could the 10-20A be a result of cryo damage as opposed to true packing
disorder? (try collecting a few images at room remp)
If its cryo damage, improve your cryo / try different cryoprotectants.
If its not cryo, just screen about a thousand different crystals from
around the same co
Good to know, thanks. I was actually wondering about this recently.
On Sun, Jan 1, 2012 at 1:14 PM, Dima Klenchin wrote:
> I've seen this happening to water molecules as well (in a somewhat
>> unpredictable fashion). In the latest refmac versions, you can try
>> harmonic restraints, although
Jiyuan,
I believe PISA will easily do this for you.
C
On Thu, Nov 10, 2011 at 5:10 PM, Ke, Jiyuan wrote:
> Dear All,
>
> ** **
>
> I have a protein that exists as a dimer in the crystal structure. I want
> to calculate and compare the area of the buried hydrophobic core of a
> monomer wi
Hello all,
Given a PDB file of a newly solved protein structure, what is the standard
procedure for assigning regions of secondary structure? And by this I mean
to ask, how does one decide which residues form beta strands, which alpha
helices, and so on? Is DSSP sufficient for this? Are we supp
Thank you to everyone who replied. I went through all the suggestions and
in the end used Jason's PyMOL script, using Thomas' cpv.distance suggestion
(which did make it much faster for me) and a few more modifications to
eliminate redundant pairing listings.
Bellow is the modified script, saved a
ipting
> possibly in python or perl. This is a tractable problem with a bit of
> scripting and if you aren't already experienced this may be a good
> opportunity to delve into a bit of programing.
> Good Luck,
> -bob
>
> On Tue, Mar 8, 2011 at 7:20 PM, Cale Dakwar wrote:
>
e PDB
structures in which e.g. the shortest His-His distances have been observed.
- C
On Tue, Mar 8, 2011 at 6:19 PM, Ed Pozharski wrote:
> On Tue, 2011-03-08 at 17:44 -0500, Cale Dakwar wrote:
> > Amongst other things, I want e.g. generate a histogram from this table
> > and determi
Hello all,
For any given structure in the PDB, I want to identify all the Histidine ND1
atoms. I then want to consider these atoms in pairs, measure the distance
in Angstroms between the ND1 atoms in each pair, and compile these distances
(along with residue numbers of the pair) in a table. I th
Dear
Dear colleagues,
Please excuse these naive questions but I am new to the field of structural
biology and need to ask it.
1) By submitting my structure to the PDB Validation Server for precheck and
validation, will my structure become publicly available in any way?
2)
When I finally submit my str
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