Absolutely. But don't bother with SIRAS: straight SAD will do the job 9/10
times these days, thanks to magnificent beamlines and algorithms.
Sent from tiny silly touch screen
From: "Whitley, Matthew J"
Sent: 22 Jun 2017 1:09 am
To: CCP4BB@JISCMAIL.AC.UK
Subject:
I second (or third) the suggestion that others have given to try soaking
mercury compounds into your crystal. Mercury absolutely loves free cysteines,
and if you have 5, you have a great chance of getting binding. If isomorphism
is maintained after soaking, the isomorphous differences will be
I figured it out. Rcrane works fine if I remove the hydrogens before going
into Coot.
Ursula
On Wed, Jun 21, 2017 at 12:04 PM, Ursula Schulze-Gahmen <
uschulze-gah...@lbl.gov> wrote:
> I am trying to use Rcrane in stand-alone coot version 0.8.8. The Rcrane
> window opens and I am able to calcula
To perform double labelling on your protein in an NON auxotrophic strain may be
difficult. For the seleomet side, you can shut down the biosynthesis of Met by
the addition of lysine, phenylalanine, threonine, isoleucine and valine;
various protocols exist online. However to shutdown biosynthesis
Dear Vito,
for SeMet have a look here:
http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Expression_of_SeMet_labeled_proteins
Worked like a charm for E.coli and also for other expression hosts
with minor modifications
(https://www.nature.com/nature/journal/v516/n7529/full/nature14003
Looks like positive cooperativity to me. If binding at one site increases
affinity at the second site, then intermediate concentrations of your
unlabelled ligand can (seemingly paradoxically) *increase* binding of your
tracer. At higher levels still, the unlabelled ligand outcompetes the tracer
Hello All,
This is an off-topic question. I have some issues regarding Fluorescence
Polarization competitive displacement assay and would need some advice.
I have developed an in vitro fluorescence polarization based assay using a
N-terminus labelled FITC peptide. The peptide is 21 amino acids lo
I'm thinking a nomenclature issue.
H5 ? Should be H5' no?
Have you run your structure through a pdb remediator?
http://kinemage.biochem.duke.edu/software/remediator.php is my favorite.
You will want to play around with the flags to get the right output. I think
rCrane likes old style nomen
I am trying to use Rcrane in stand-alone coot version 0.8.8. The Rcrane
window opens and I am able to calculate new conformations for my nucleic
acid. But when I am trying to accept a conformation, I am getting an error
message:
Traceback (most recent call last):
File
"/home/programs/x86_64-linu
I am trying to use Rcrane in stand-alone coot version 0.8.8. The Rcrane
window opens and I am able to calculate new conformations for my nucleic
acid. But when I am trying to accept a conformation, I am getting an error
message: Key Error "H5". Any suggestions what might be wrong, and how I can
fix
Something like Balbes for MR is worth a shot? I wouldnt bother manually with MR
anymore unless really clear. Or try Hg and Pt for Cys, His and Met. I would try
the Pt chlorides. All depends on pH etc...
Tommi
Alkuperäinen viesti
Lähettäjä: "Keller, Jacob"
Päivämäärä: 21.06.2
Halide soaks anyone? Cs or NaI?
Jacob
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Mark J
van Raaij
Sent: Wednesday, June 21, 2017 12:08 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Se-Met and Se-Cys double labelling
If your data is good enough, your SeMets alone
If your data is good enough, your SeMets alone might well be enough.
Soaking native crystals in Hg compounds may also work, avoiding SeMet
altogether. We have had a lot of success with methylmercury chloride binding to
free Cys. You may have to experiment with different soaking times and protocol
I am working on a protein having 360 residues. In its sequence there are 3
Met and 5 free Cys.
I will need MAD to solve the structure since based on the sequence the
closest homologue has 20% identity
I suppose MR would be very unlikely to
work
so I would like to express a selenium derivative to ex
Hi, all
I am running Blend on a new machine (Redhat 6.9 Santiago) and met the
following X11 module and R code error. Thanks for your help.
When I run
$ X -version
It returns:
X.Org X Server 1.17.4
Release Date: 2015-10-28
X Protocol Version 11, Revision 0
Build ID: xorg-x11-server 1.17.4-
Dear Chen,
Is this an icosahedral virus crystal structure, or a highly symmetric structure
where the RNA may have different binding modes to each subunit and thus
averaged out in the crystal?
Best wishes,
Reza
Reza Khayat, PhD
Assistant Professor
City College of New York
Department of Chemistr
We have sometimes used Michael Garavito's excellent suggestion of diffusing
glutaraldehyde into the drops - mentioned on this board a few days ago.
Our protein crystals either turned brown or turned into brown goo.
Michael and others, what effect would you expect glutaraldehyde to have on
DNA crys
Dear Chen,
I will answer with some question :
- How is the refinement going ? Is the RNA properly taking in count ?
Which soft do you use ?
- How do you solve the structure ? MR ? If it's MR did you use a model
which contain both protein and RNA ? Did you try to solve with the
protein only
Dear All,
We have get a complex crystal and the resolution can be refined to nearly 1.84
Å. But the electron density of the RNA is very weak.
In some datasets we can't find any density of the RNA and in other datasets we
can see more or less some RNA density.
For now we can build 6-7 nucleoti
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