Dear All,
After we refine the structure of the protein to satisfactory with
satisfactory Rwork and Rfree, we pick water by phenix refine, and I find Rfree
always increases slightly after the water picking refinment.
Do you have nay idea to solve this problem or any comment?
Cheers,
Rationalising it completely may only be possible once you know the nature of
the crystal contacts, i.e. when you have solved the structure. Until then it is
mainly a matter of experimenting.
-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
Hi,
I think your 64bit system lacks the 32bit loader. Try as root:
yum install /lib/ld-linux.so.2
and be prepared to install a couple of 32bit libraries, as needed.
HTH,
Kay
Original Message
Subject: tcl tk RHEL 6.2
Date: Mon, 6 Feb 2012 10:17:22 -0600
From: Kenneth A.
Dear colleagues,
I am looking for a few example studies in which a complete mutagenesis
of all residue-ligand interactions has been conducted to evaluate the
energetic contributions of each individual interaction.
Thank you.
Best regards.
-Chris
Dear Chris
A whole series of studies from the early to late 90's did his for the growth
hormone-GHR interaction.
Papers by Pearce, Cunningham, Clackson and Wells come to mind.
Also a recent study on the IL13-IL13R interaction by Lupardus et al has covered
most of the interaction epitope.
On 02/07/2012 08:31 AM, Dialing Pretty wrote:
Dear All,
After we refine the structure of the protein to satisfactory with
satisfactory Rwork and Rfree, we pick water by phenix refine, and I find Rfree
always increases slightly after the water picking refinment.
Do you have nay idea to solve
Hi Dialing,
Most water picking tools are rather overenthusiastic and end up placing some
waters at places where they should not be. This causes some overfitting and
an increase of R-free. I'm hideously old-fashioned and recommend
conservatively building waters by hand.
There are some good
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
Dear Deepak,
the only atom type present in DNA and not in Proteins would be the
Phosphorus. You can probably add this to sc_radii.lib yourself with the line
***P* 1.80
the radius stems from http://en.wikipedia.org/wiki/Phosphorus and the
Hi,
I am forwarding an announcement for a permanent scientist position in
structural biology using SAXS
at the synchrotron SOLEIL located in Paris suburbs, France.
Please address all questions concerning the position to the responsible
: Dr. Javier PEREZ pe...@synchrotron-soleil.fr
Best,
Dear colleagues,
We have solved the crystal structure of a human enzyme. The pKa of a
catalytically critical aspartic acid has increased to 6.44. It is hydrogen
bonded (2.8 Angstroms) to a water molecule that is supposed to donate a
proton during the catalysis. Can anybody help me a) interpret
Hi CCP4 list,
Thank you very much for additional messages and references.
Here goes the image of the PCR product before digested and after
digested and cleaned.
http://ompldr.org/vY29jbA
The results of the transformation of 3 microL (90 ng) of
non-mutated/paretal plasmid gave hundreds of
Hi Deepak,
Assuming that you have done the necessary things to measure the pKr of
that particular Asp, I would say that the increase is advantageous for
your enzyme. Enzyme catalysis often involves very subtle changes on the
ionization state of the active site. But you need to be very careful
One last thing--sometimes crystals can be frozen as is, particularly
if you use mitegen mounts and get nearly all of the mother liquor off
the crystals by dabbing the loop on the dry surface next to the drop
several times. So simple it is always worth a try
JPK
On Tue, Feb 7, 2012 at 2:37
Hi Fred:
For the mutated plasmids, it generates the nicked dna, so the transform
efficiency will be lower compared to the parental plasmids. And that is the
reason why people usually use super competent cell to transform these nicked
plasmid. It seems ok to me to get 2 or 14 colonies from the
Hi Deepak:
I think it is common for the residues which participate catalysis to have a Pka
deviated from the reality pKa value especially for acid/base catalysis (acid
base titration assay can help you to figure out the way of catalysis). Usually
the pKa values of these kind of critical
Residue pKa values in proteins are strongly
affected by the local environment and can deviate far from the
"norm". Of course, the higher the pKa of the residue, the stronger
general base it will be. There is a significant
thermodynamic/kinetic advantage in
Something to add into this discussion is also go fro the tiny crystals versus
the big ones.
BIGGER is not always BETTER - in particular if you try to freeze directly out
of your conditions without an additional cryo-protectant. And with small or
tiny I mean 10 micron, whatever you are capable
Dialing,
After we refine the structure of the protein to satisfactory with
satisfactory Rwork and Rfree, we pick water by phenix refine, and I find Rfree
always increases slightly after the water picking refinment.
Do you have nay idea to solve this problem or any comment?
Just a reminder:
As we know, the pKa of water is 15.7. Under pH 7.0, its protonation
should be 50/50.
In this case, we may need to consider water in two formats:
H2O vs. H3O+
When we say water as acid, it usually stands for H3O+ in chemistry. In
chemical equation, H+ represents H3O+.
In enzyme catalysis, water
Check this review, for instance:
Pace, C. et al. Protein Ionizable Groups: pK values and Their Contribution to
Protein Stability and Solubility. J. Biol Chem. 284, 13285-13289 (May 15,
2009)
Thierry
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK]
Oops, you meant catalytic residue. Check the following:
Harris TK Turner GJ Structural basis of pertubed pKa values of catalytic
groups in enzyme active sites IUBMB life, 53 85-98 (Feb 2002)
Thierry
From: Fischmann, Thierry
Sent: Tuesday, February 07, 2012
BIGGER is not always BETTER?
Theoretically it should be better because you have more scattering matter.
If it is
not something has gone wrong in prior steps:
Purification: You were less selective and picked up more heterogeneous
protein.
Crystallization: The bigger crystals grew under
Hi,
you may also look into the papers of John A. Gerlt, who did a lot on
protonabtraction reactions and the theory behind this. Esspecially the pKa
disturbance and the match to the pkA of the substrate of the reaction.
Best Wishes
Christian
Am Dienstag 07 Februar 2012 12:48:26 schrieb
Hi Enrico,
I was just looking at non-optimal cryo-conditions and the original posters
starting point.
Of course if you have a good cryo bigger is better for the reasons you write
but if you have no clue how your crystals will perform then I'd rather go for
small to be cautious and also have
Is the water molecule in question coordinated to any other group(s)?
-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Kevin
Jin
Sent: Tuesday, February 07, 2012 10:22 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] On pKa of Aspartic acid
As
We have a high and low res pass on a crystal that is going to around 1.2 A on
the pilatus at Diamond.
We tried to scale them together using the xds CORRECT files from the xia2 -3dii runs (gives best results as far as we
can see comparing xia2.html files) through aimless via ccp4i interface.
Maybe you would also be interested in
http://www.jinkai.org/AAD_history.html
Regards,
Kevin
On Tue, Feb 7, 2012 at 8:52 AM, Christian Roth
christian.r...@bbz.uni-leipzig.de wrote:
Hi,
you may also look into the papers of John A. Gerlt, who did a lot on
protonabtraction reactions and the
Dear Jürgen,
Am 07.02.12 16:58, schrieb Bosch, Juergen:
snip
Then one last remark, LN2 versus cryo-stream freeze. Dipping in LN2
leads to a quicker freeze of your material.
/snip
Are you sure? There was a publication by Warkentin et al. [1] about a
cold gas layer above liquid nitrogen that
Hi Dirk,
I remember a neat paper don't recall who wrote it. I think it was in Acta D
where the authors made a tiny probe the size of an elongated crystal glued to a
[/Advertisement on] Hampton loop [/Advertisement off]. The probe was a
temperature sensor and they recorded the cooling rate
Hi Deepak,
With regards observed pKa shifts, Prof. Ondrechen from Northeastern University
has had a long interest in this field.
http://www.northeastern.edu/org/wp/
Under the computational tools that she has developed a program called THEMATICS
that allows you to predict the pka of titratable
Just a thought for those that mentioned propane and ethane, I would like to
suggest that they try carbon tetrafluoride (CF4) instead. It certainly should
be much safer. It melts at 90 K and boils at 145 K, so you know you are below
145 K if you see it as a liquid.
On 02/07/12 11:12, Dirk Kostrewa wrote:
Dear Jürgen,
Am 07.02.12 16:58, schrieb Bosch, Juergen:
snip
Then one last remark, LN2 versus cryo-stream freeze. Dipping in LN2
leads to a quicker freeze of your material.
/snip
Are you sure? There was a publication by Warkentin et al. [1] about a
Jürgen Quote: Propane for whatever reason has gone extinct in certain
areas of the world :-) .
I went to SSRL (Stanford) with a colleague who wanted to use liquid
propane. We had to go through a mound of paper work to get permission
bring propane on site and set up the experiments. I
This job was posted earlier, but there is an update to the how-to-apply
instructions.
The Macromolecular Diffraction Facility of the Cornell High-Energy Synchrotron
Source (MacCHESS) has an opening for a Staff Scientist (Research Associate) to
pursue the development of novel techniques in x-ray
Hi Kevin,
Hate to point this out, but under pH 7.0, the protonation state of water is not
50:50, and it is not a good acid. The H30+ concentration of pure water is
10^-7 Molar. In pure water (assuming 55.5 M) only 1:555,000,000 water
molecules is in the protonated, charged state (H3O+).
Hi,
from your description I do not quite understand a few points:
- what is the evidence that there are overloads? The Pilatus pixels have
20bits (meaning max contents of a pixel = 1048575) , and the OVERLOAD
parameter is set to 1048500 (slightly below that). Do you actually see
pixels with a
Oops, It should be: [H3O+]/[OH-]= 50/50
Kw = [H3O+][OH-],
pH = pKa +log ([OH-]/[H2O])
H3O+ concentration of pure water is 10^-7 mol/L
total H+ = 55.5M * 10^-7 = 5.55* 10^-6 mole. Is this right?
Regards,
Kevin
On Tue, Feb 7, 2012 at 12:13 PM, Zachary Wood z...@bmb.uga.edu wrote:
Hi Kevin,
Dear CCP4BB,
this is perhaps my most egregious off-topic post, but can anyone
explain why the following reference is not findable in PubMed? I can
get it from the ACS website, but not on PubMed or elsewhere. The
journal is on PubMed--is it perhaps because it's funded by ExxonMobil?
Very
No. Kw = [H3O+][OH-] = 1 x 10^-14 at 25 deg C.
So at pH 7.0, you have 10^-7 M each at
equilibrium no matter how you slice it or whatever else is in
solution. If equilibrium [H3O+] goes up [OH-] goes down
commensurately.
The "pKa" of water as
Dear all,
for further discussion
I believe that using the 0-14 pH scale assumes water activity of pure
water, something that is surely not matched in the surface or pocket of a
protein, so keeping this in mind I always prefer to speak about apparent
pKa of a group if talking about a non
On 2/7/12 4:02 PM, Jacob Keller wrote:
Dear CCP4BB,
this is perhaps my most egregious off-topic post, but can anyone
explain why the following reference is not findable in PubMed? I can
get it from the ACS website, but not on PubMed or elsewhere. The
journal is on PubMed--is it perhaps because
Hi folks,
I have an intriguing problem. I'm trying to generate a cif file for a
macrocyclic peptide (of the likes in
pdb1d4khttp://www.rcsb.org/pdb/explore/explore.do?structureId=1d4k). They are
cyclic tripeptides units. I can generate a pdb or mol2 file easily. I have used
PRODRG to generate
This might be obvious, but make sure you washed the crystals
thoroughly before dissolving them for SDS-PAGE or mass spec
-Jesse
On Thu, Jan 26, 2012 at 10:48 AM, Katherine Sippel
katherine.sip...@gmail.com wrote:
Might I suggest consulting the CCP4 user community wiki on the topic:
Well, perhaps it is because size exclusion chromatography is used so
little in the life sciences؟, and who really cares how it works
anyway?؟
JPK
On Tue, Feb 7, 2012 at 3:18 PM, Matthew Franklin mfrank...@nysbc.org wrote:
On 2/7/12 4:02 PM, Jacob Keller wrote:
Dear CCP4BB,
this is perhaps
The MacCHESS BioSAXS Essentials minicourse filled up just a few days after we
made the announcement over a week ago. Hopefully the overflow will find their
way to Brookhaven and other places. To date, there has NOT been a lot of
interest among potential organizers in holding such a course at
Hello,
After following the discussion on
[ccp4bb] shape complementarity between protein and DNA surface,
is there someone here able to explain simply what the SC software
of CCP4 is calculating?
I mean, is there some intuitive/easy to understand explanation of what
SC is calculating?
I know
This looks like one of those journals not routinely indexed by the NLM. There
are some issues in Medline, but not all. I only found one article from 2004.
http://www.ncbi.nlm.nih.gov/nlmcatalog/365316
John
Sent from my iPad
On Feb 7, 2012, at 4:02 PM, Jacob Keller
I'm going with Jurgen on this one.
http://img27.imageshack.us/img27/3232/pastedgraphic1.png
Sad was the day when I mounted this puppy and it shot to 8-10A. Room
temperature. And messing around with cryos didn't help either.
Can't remember the size, but I think I had scooped it with a 0.8
Sad was the day when I mounted this puppy and it shot to 8-10A. Room
temperature. And messing around with cryos didn't help either.
But if that puppy had been smaller, it might have diffracted even
worse, and just think if that little icy crystal had been bigger...
JPK
Can't remember the
...a weight is lifted off my shoulders
http://www.flipperkiste.de/work.link.php?jgyahooID=65l2
Hi Francois
Here's a one-liner. The major concept behind the Sc coefficient is that it
measures the extent to which, on average, the normal vectors between
closest-neighbour opposing points within the molecular interface are
antiparallel.
Sc=1 implies that the surfaces fit exactly, all such
On 02/08/2012 12:47 PM, Mike Lawrence wrote:
Hi Francois
Here's a one-liner. The major concept behind the Sc coefficient is that it measures the
extent to which, on average, the normal vectors between closest-neighbour
opposing points within the molecular interface are antiparallel.
Sc=1
Hi all,Please don't click on any links in emails from me, my hotmail password
was compromised and it emailed my entire address book malicious links.Hope
everyone is well!Krystle
--
Krystle J. McLaughlin, Ph.D.
SPIRE Postdoctoral Fellow
Redinbo Group, Department of Chemistry
University of
Bosch, Juergen wrote:
Hi Dirk,
I remember a neat paper don't recall who wrote it. I think it was in Acta D
where the
authors made a tiny probe the size of an elongated crystal glued to a
[/Advertisement on]
Hampton loop [/Advertisement off]. The probe was a temperature sensor and they
Dear all,
I have a 17 KDa protein that gives crystals in a condition that has
0.1M bis-tris pH 6.5. The crystals are thin needle clusters and do not
diffract. I have tried additives, but they haven't improved the crystals. I
intend to vary the pH of the condition.
My
Dear Sreetama,
First of all, there are no hard-and-fast rules for successful
crystallisation, try changing as many different variables as possible
and go with what works.
Having said that, yes, next I would go for a grid optimisation varying
the pH in 0.2 or 0.5 units over as wide a range
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