Alastair Fyfe wrote:
Does anyone know of software that will segment a unit cell into volume
internal/external to a calculated molecular surface ?
thanks!
Alastair Fyfe
Well, if the surface was generated from some sort of model it is easy to
mask the unit cell map to set all the volume
As far as I know all the programs we use will handle the non-primitive
hexagonal setting of rhombohedral space groups (ie a=b != c, alpha=beta=90,
gamma =120), often denoted H3 or H32 (aka R3:H in cctbx). Many of them will
probably handle the primitive rhombohedral setting (a=b=c,
Hi Tony,
in my experience it is not uncommon for crystals that diffract to
resolution worse than 3 A to be anisomorphous - after all, there is a
reason for diffracting badly, and that must be the lattice defects.
Lattice defects e.g. often lead to differences in cell parameters, and
in that case
Hi everybody,
I just solved the structures of an enzyme an some variants. In the active site
cavity of each variant I found one or two fragments of PEG1000 bound. I used
PEG1000 in the crystallization condition. Among the enzyme variants the number
of non-hydrogen atoms of these PEG fragments
Dear Klaus
depends how many missing residue you want advertised in the
header of your deposited file. The pdb will put in a special Remark 610 and
Remark 615 to indicate any missing residues from your heterogen list. However
the policy is not to list every missing (or zero
The Protein Data Bank in Europe (PDBe; http://pdbe.org/) offers a number of
educational resources as part of its wider mandate for outreach and training
within the European Bioinformatics Institute (EBI; http://www.ebi.ac.uk/).
As part of this commitment, we offer the PDBe roadshow
Coming from small molecule crystallography where this problem simply
doesn't exit, I found it very difficult to understand all the fuss!
The small molecule crystallographers specify the symmetry operations
rather than the space group so there is nothing special about using
different settings. If
Hi Ray,
In HKL2000, by default (i.e. - without changing anything manually) for R32/H32,
Denzo/Scalepack leads to a .sca file that has hexagonal unit cell parameters in the
header but has the space group listed as R32. Scalepack2mtz in ccp4 does not like this
mismatch so you have to simply
Dear All,
I am refining structure of protein at 1.7A. It is enzyme with 3
histidine residues in the active site, which are chelating metal (at
the moment I built in calcium but I do not know for sure, which metal
is bound there). I can see additional density on top of metal, which
I can
Take a look at MAMA from Uppsala Software Factory
http://xray.bmc.uu.se/usf/mama_man.html
It can generate the mask from the PDB file. This will, however, leave
internal cavities belonging to solvent. If you don't want that, the
following MAMA script will fix it giving you the mask of the
PEG solutions contain fragments of all sizes - it is the average size
(however defined by the manufacturer) that is 1000. So technically it
is incorrect to claim that you have PEG1000 molecules bound to your
protein, it is most likely much shorter fragments that can penetrate the
channels in
On Thu, 2010-08-12 at 08:57 +, MARTYN SYMMONS wrote:
Zero occupancy is generally a deprecated way of dealing with missing
density as it is confusing for less experienced user of the
coordinates. I think zero occupancy can be useful during refinement as
the atoms help fill space (or for
Nevertheless, what do you have in mother liquor/protein buffer?
On Thu, 2010-08-12 at 17:24 +0200, wrote:
Dear All,
I am refining structure of protein at 1.7A. It is enzyme with 3
histidine residues in the active site, which are chelating metal (at
the moment I built in calcium but I do
Hi,
Is there any server or program can calculate the theoretic PKa of the
protein-DNA complex? Given the structure of the protein and the
sequence of the DNA. Any suggestion will be appreciated!
Best
Yang
Could this be a metal cluster? Is your protein solution colored at all? Have
you made an anomalous difference map? Is there reductant in the mix? What
small molecules were in the mother liquor?
JPK
- Original Message -
From: Justyna Wojdyla ty...@embl-hamburg.de
To:
Hi Matt,
Check out the following paper and some screens available commercially based on
these:
Acta Crystallogr D Biol Crystallogr. 2004 Sep;60(Pt 9):1670-3. Epub 2004 Aug 26.
Optimum solubility (OS) screening: an efficient method to optimize buffer
conditions for homogeneity and
Hi Matt,
Have you tried changing the pH? Is it possible that at pH 8 you are at
the pI of your protein (i.e. where it has zero net charge and is at
its least soluble) ?
I have also read a paper (can't find the reference right now) where
the authors precipitated their protein by dialysing into
That's a good point, Ed
Based on the formula: HO CH2-(CH2-O-CH2)n-CH2OH, PEG MW = 44n+62, a table of n
to MW goes like below which gives an idea of what range is possible. Someone
maybe knows what polydispersity can be expected from the synthetic process. As
you say though, a specific range
Dear All,
In order to phase, I intend to derivatize my protein(30kDa)-DNA(7.2kDa)
complex with heavy atoms. I wanted to know which was the better way to do
it: longer soaks at lower heavy atom concentration, or shorter soaks with
higher concentration of heavy atom. Also, what concentrations and
Googling peg polydispersity returns this as the second hit
http://www.springerlink.com/content/tp643l7678048447/
which is circa 1973 data from behind the iron curtain. The technology
may have improved, and the most recent I can quickly find is this paper
Plata et al., Electrophoresis, (2010),
Hi all.
I found that reference. :0)
Acta Crystallogr D Biol Crystallogr. 2006 Jul;62(Pt 7):833-42. Epub 2006 Jun 20.
Assessment of a preliminary solubility screen to improve
crystallization trials: uncoupling crystal condition searches.
Izaac A, Schall CA, Mueser TC.
Hi Amit,
For heavy atom phasing, you'll have to try all the things you can, limited
only by supply of crystals, availability of heavy atoms (and considering heavy
atom handling and waste disposal policies for solutions, tips, etc.) and time
and effort.
I had success with both short soaks
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