Dear ccp4 users,
does anyone know if there is a way to (re)calculate the Rmerge from a
deposited .cif file in PDB?
In this case is an already merged structure factor file.
I know that the EDS from Uppsala makes it, providing the PDB entry, but I
need a procedure in order to do it by myself.
I
I think the name says it all:
Rmerge
merged data
So no, there wouldn't be. You'll find it in the header.
On 30/01/2014 08:18, Fulvio Saccoccia wrote:
Dear ccp4 users,
does anyone know if there is a way to (re)calculate the Rmerge from a
deposited .cif file in PDB?
In this case is an
Dear Roger,
The Phaser developers contribute Phaser to both CCP4 and Phenix, so it's better
to contact us directly rather than, say, going through the phenix help,
especially if it's a CCP4 specific issue.
The syntax of the call to HySS in the Phaser SAD phasing pipeline hasn't
changed for at
Hi Shane,
another curious case is the crystal structure of a signal receiver domain of
Desulfovibrio desulfuricans (PDB code: 3cg0, Patskovsky et al., to be
published), as discussed in Sippl (2009) Curr. Opin. Struct. Biol.
Best,
-Markus
Hi ccp4bb,
I'm putting together a talk for some
There is one additional point perhaps worth making: As already noted in the
thread, if you have a NCS homo-oligomer, the different copies in general
have different environment, and proper inspection of the contacts reveals
the details. On multiple occasions during inspections and review I have
Insulin can take very different structures for 20% of the residues in
different conditions, and there are several examples of T3R3
hexamers, with one T and one R in the asymmetric unit. There are
even observations of the transformation occurring within the crystal,
which looked battered but still
I am afraid there is no real solution except to read the paper!
And even that doesnt help if you suspect the merging..
There is lots of discussion about the merit of depositing UNMERGED
data - and that would certainly help developers. Add your voice to the
request!
Eleanor
On 30 January 2014
Dear All,
This may be slightly off-the-track question but your feedback will be very much
appreciated. The situation is-
I obtain a very low amount of the protein of my interest (a hetro-dimer) from
the construct I am using (only 8% of the total amount of protein obtained is
the protein of my
The easiest way to produce repeatable conditions is to titrate a stock
solution (say 1M) of citric acid with NaOH to the desired pH and use that
to mix your screen. That's what Hampton does anyway.
If fine sampling pH, you can mix various ratios of pH 3 and 6.5 buffers.
The pH won't be linear
hello Andy,
i have different questions about your problem :
Is the hetero-dimer co-expressed ? Or the two partners are express separately ?
Have you controlled where are you proteins after the lysis, because if you
have many of your proteins in the pellet, it's not a good sign for the folding
Do you really need to remove the NaCl? Some ionic strength is often
necessary to stabilize proteins. Our routine purification buffers all
contain at least 100 mM NaCl. This will not usually interfere with
crystallization screening.
To minimize the probability of aggregation, you need to (1)
It’s a pain but I usually just make each pH of whatever buffer I’m using (if
you make it concentrated then you’ll only have to do it once). Also, if you
haven’t already found it, Hampton has a nice link to calculate volume of
components while designing a tray as long as you tell it the
Dear All,
1st of all , Thanks for the very quick feedback. I will answer your questions
to make the picture more clear-
Nicolas-
Yes the dimer is co-expressed. Almost all the protein is in the sup and not in
the pellet. Multiple-step dialysis has failed. I have been trying various
controls
But you have to be aware that pH depends on the concentration of the
buffer. This is especially the case for phosphate and citrate buffer.
Daniel
Le 30/01/2014 15:51, Schnicker, Nicholas J a écrit :
It’s a pain but I usually just make each pH of whatever buffer I’m
using (if you make it
Alternatively you could make a stock solution of citric acid (say 1 M for
example) and stock solution of sodium citrate (also 1 M). Mix them in the
appropriate ratio to ballpark the right pH and just adjust up or down with
the stock solution. The concentration of citrate will be the same no matter
Dear all,
This july, an exciting Summer School will take place at Les Houches in the
Chamonix Valley, France. It will deal with Integrated Structural Cell Biology
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Dear CCP4bb,
If you are a talented and motivated postdoctoral structural biologist, or soon
to be, or know somebody who is…
Project Title: Structure and function of the essential M2-1 protein of human
respiratory syncytial virus
Our laboratories are interested in understanding the structural
RE citrate buffer preparation
The Calbiochem buffers has some generally useful information about
buffers; pKa and such.
http://www.antibodybeyond.com/books/Calbiochem_Buffers_Booklet_CB0052_E.pdf
http://wolfson.huji.ac.il/purification/PDF/Buffers/Calbiochem_Buffers_Booklet.pdf
--
Hi Sreetama,
For most buffers, I use Katherine's method, but in the case of citrate I'd
recommend just titrating citric acid with NaOH. I've made a pH series from
citric acid and Na3Cit before, and it's a huge pain. It's very difficult to
calculate how much of each you'll need, because citrate is
You are correct about certain buffers as interferents. Certain buffer
species will coordinate with or precipitate silver or mercurous ions
that are present in the reference electrode compartment of the
combination pH electrodes. Tris is notorious for clogging the little
porous frit on the
If the pK's are well separated, so that only one is titrating at a time ( assume
only two species exist at a time), the number of equiv of NaOH to add would be :
1/(1+10^(pK1-pH)) + 1/(1+10^(pK2-pH)) + 1/(1+10^(pK3-pH))
where each term transitions from 0 to 1 as pH passes through it's pKa
In
Dear all,
We are holding a webinar next week (Feb 4th 9AM PST) highlighting the
tools available in our free molecular visualization software tools-
ICM-Browser (Desktop - Win/Mac/Linux), iMolview (iPad/Android), and
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