As the macromolecular crystallography becomes more automated and
user-friendly many biologists learn to solve structures and they can
make mistakes. Besides, new data become available that can give new
ideas etc. I don't think that's so horrible to make an honest mistake
and retract papers. Eve
Hi,
We had a paper where we looked at Kd of arginine in the arginine
repressor-DNA complex (p. 248-249).
JMB,2010, *399*, pp.240-254.
Maia
Jacob Keller wrote:
Yes, I think you are right--the somewhat counterintuitive case I was
thinking of was, for example, when:
Kd = 20nM
[L] = 20uM
[Po i
Hi Nigel,
I need to make a cif file for a gold ion, Au1+, no other atoms. It is
covalently attached to sulfur of cysteine
in two conformations. So, how do I label Au+1 with A and B
conformations. How to make a cif for this.
Maia
You probably use hanging drops. It's the surface tension effect. Check
if sitting drops are better.
Maia
Sitting drops
weikai wrote:
Hi Folks,
We have some membrane protein crystals that are grown in 30%PEG400,
0.1M Na Citrate pH 4.5, 0.1M LiCl. The protein is purified in DDM. The
crystals
I guess, most hydrophilic side chains on the surface are flexible, they
don't keep the same conformation. If you cut those side chains off, the
surface will be looking pretty hydrophobic and misleading (and very
horrible). I prefer to see them intact. I know, most of them are
flexible and don't
process
for you.
Maia
On 21/03/2011 4:33 PM, Maia Cherney wrote:
Hi PS
What is the unit cell dimensions in the first crystal? It looks like
protein to me.
Maia
On 21/03/2011 2:03 PM, Pius Padayatti wrote:
Hi all,
We recently observed some diffraction from membrane protein
crystallization
Hi PS
What is the unit cell dimensions in the first crystal? It looks like
protein to me.
Maia
On 21/03/2011 2:03 PM, Pius Padayatti wrote:
Hi all,
We recently observed some diffraction from membrane protein crystallization
drops diffraction that look like non-proteinaceous (please see at
Hi James,
I remember that P1 did not help. That was like 2 years ago. That crystal
was very important at that time, so I had to use it. There were many
other crystals since then (native, mutants and complexes) in the same
space group without problems. But also I had even a more weird crystal
- Original Message
> Subject: [Fwd: Re: [ccp4bb] I/sigmaI of >3.0 rule]
> Date: Thu, 3 Mar 2011 10:45:03 -0700
> From: Maia Cherney
>
>
>
> Original Message
> Subject: Re: [ccp4bb] I/sigmaI of >3.0 rule
> Date: Thu, 03 Mar 2011 10:43:23
n Thu, Mar 03, 2011 at 10:57:37AM -0700, Maia Cherney wrote:
I see, there is no consensus about my data. Some people say 2.4A,
other say all. Well, I chose 2.3 A. My rule was to be a little bit
below Rmerg 100%. At 2.3A Rmerg was 98.7%
Actually, I have published my paper in JMB. Yes, reviewers di
makes sense to select a higher cutoff
(like what exactly?) and reprocess the data. Maybe one of our data
collection specialist should comment on that.
BR
-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Maia
Cherney
Sent: Thursday, March 03, 2011 9:1
Original Message
Subject:Re: [ccp4bb] I/sigmaI of >3.0 rule
Date: Thu, 03 Mar 2011 10:43:23 -0700
From: Maia Cherney
To: Oganesyan, Vaheh
References: <2ba9ce2f-c299-4ca9-a36a-99065d1b3...@unipd.it>
<4d6faed8.7040...@ualberta.ca>
<021
I have to resend my statistics.
Maia Cherney wrote:
Dear Bernhard
I am wondering where I should cut my data off. Here is the statistics
from XDS processing.
Maia
On 11-03-03 04:29 AM, Roberto Battistutta wrote:
Dear all,
I got a reviewer comment that indicate the "need to refin
Dear Bernhard
I am wondering where I should cut my data off. Here is the statistics
from XDS processing.
Maia
SUBSET OF INTENSITY DATA WITH SIGNAL/NOISE >= -3.0 AS FUNCTION OF RESOLUTION
RESOLUTION NUMBER OF REFLECTIONS COMPLET R-FACTOR R-FACTOR COMPARED
I/SIGMA R-meas Rmrgd-F Anomal SigAno
Original Message
Subject:Re: [ccp4bb] Space group and R/Rfree value
Date: Wed, 01 Dec 2010 09:44:06 -0700
From: Maia Cherney
To: Xiaopeng Hu
References:
<643947201.129232.1291191478190.javamail.r...@zmbx0.sysu.edu.cn>
A dimer could be with a sy
I found a practical solution to a similar problem. When I get large
gap between Rf/R in refmac I repeat the refinement in PHENIX using the
same model and the same mtz file, It has always worked for me. And I
have no theory for that observation, but the tables in publications
looked better.
I had a similar problem. It dissappeared when I switched the
refinement to phenix. The R factors dropped and the difference between
them became acceptable.
Try balbes from G. Murshudov's website. It will find proper search model
and use proper truncations automatically. In addition, it will put in
your sequence.
Paul Holland wrote:
Hello fellow crystallographers,
I am trying molecular replacement for a protein crystal dataset that has very
high
Hi ccp4bb
Could you please send me some references with the sedimentation
equilibrium calculations of Kd, monomer/dimer ratio etc.
Maia
Maia Cherney wrote:
Thank you. Now I understand the difference. I thought there was
separation.
Maia
Xuewu Zhang wrote:
Hi Maia,
I have seen your post
Thank you. Now I understand the difference. I thought there was separation.
Maia
Xuewu Zhang wrote:
Hi Maia,
I have seen your post regarding this before and I just want to point
out that you may have confused "AUC" (analytical ultracentrifugation)
with gradient-based ultra-centrifugation meth
To determine the oligomeric state of a protein (monomer or dimer in your
case), it's useful to use the PISA server. You upload your pdb file from
the crystal structure.The server calculates the areas of interfaces
(buried area) and deltaG (change in Gibbs energy) upon oligomer
dissociation. (E
Try balbes. It needs only your sequence and your mtz file.
http://www.ysbl.york.ac.uk/~fei/balbes/
Maia
Paul Lindblom wrote:
Hi everybody,
I just crystallized a new project protein. How can I find a possible
model for using molecular replacement? I have the sequence of my
protein. Is it e
Original Message
Subject: Is it possible for the Tris buffer to strip the Zn ions from
the Zinc Finger motif of a protein?
Date: Sun, 23 May 2010 08:45:55 -0600
From: Maia Cherney
To: ruheng
The complex can dissociate without loosing Zn. For example, if you
.mac.com/bosch_lab/
On May 19, 2010, at 1:31, Maia Cherney wrote:
Dear Jacob, I offer you my opinion.
Are you talking about electrophoresis? As far as I know it does not
work
for the mass. The velocity of a protein depends on the charge at a
particular pH, the mass and shape of molecules etc. I
You absolutely right, I thought about it.
Maia
Marius Schmidt wrote:
Interestingly, Maxwell's demon pops up here, wh... ,
don't do it.
If you change the reaction rate in one direction 1000 times slower
than
in the other direction, then the reaction becomes practically
irreversible
, at 1:31, Maia Cherney wrote:
Dear Jacob, I offer you my opinion.
Are you talking about electrophoresis? As far as I know it does not work
for the mass. The velocity of a protein depends on the charge at a
particular pH, the mass and shape of molecules etc. It's very difficult
to take al
Dear Jacob, I offer you my opinion.
Are you talking about electrophoresis? As far as I know it does not work
for the mass. The velocity of a protein depends on the charge at a
particular pH, the mass and shape of molecules etc. It's very difficult
to take all these things into consideration. O
e
the transition state less stable when approached "from the left" without
making it less stable when approached "from the right".
Dale Tronrud
On 05/18/10 12:34, Maia Cherney wrote:
If you change the reaction rate in one direction 1000 times slower than
in the other dir
If you change the reaction rate in one direction 1000 times slower than
in the other direction, then the reaction becomes practically
irreversible. And the system might not be at equilibrium.
Maia
R. M. Garavito wrote:
Vinson,
As Dale and Randy pointed out, you cannot change the ΔG of a rea
I think that it's possible to do a mutation that affects only one way of
the reaction. You can mutate a residue that makes contacts only with the
product of the direct way or only of the reverse way.
Maia
Randy Read wrote:
Dear Vinson,
I would agree with you on choice B. There are probably
s
it independent of the intel libraries which most people (notably non-developers)
probably don't have on their system.
Cheers, Tim
On Fri, Apr 30, 2010 at 12:53:49PM -0600, Maia Cherney wrote:
Hi bb,
when I try to run al3 (align) I get the error message
error while loading shared librar
#x27;-static-intel'. This doesn't alter the functionality of the program
and makes
it independent of the intel libraries which most people (notably
non-developers)
probably don't have on their system.
Cheers, Tim
On Fri, Apr 30, 2010 at 12:53:49PM -0600, Maia Cherney wrote:
Hi
Hi bb,
when I try to run al3 (align) I get the error message
error while loading shared libraries: libcxa.so.5: cannot open shared
object file: No such file or directory
In fact, this file exists. How can I tell al3 where to look for this file?
Maia
Ed Pozharski wrote:
On Fri, 2010-04-30 at
I think cacodilate is less likely because it's negatively charged as the
carboxy groups that surround the density.
I think it's Zn or it may be another (endogenous) metal ion like Ca. You
need to look at the coordination.
Maia
David Schuller wrote:
The figures would be more helpful if you tol
It's hard to see clearly the density, but judging from the abundance of
carboxy groups, it may be a metal.
Maia
Daniel Bonsor wrote:
Hello again
I currently have some unexplained density in my structure. As you can hopefully
see from the images (see file), the density is dumbbell shaped. Wha
d be in the
log file. You also nay be missing a required package, eg gcc or
something like that.
Roger
On 4/16/10, Maia Cherney wrote:
Hi Roger,
Thank you for your help.
I got this error message in the terminal when I ran ./configure.
Home-desktop:/usr/local/pdb2pqr-1.5# ./configure
checking
I know two programs;
3DNA by Lu and curves by Lavery and Sklenar. 3DNA is easier to use, it
can also make input for the Curves.
Maia
Alessandra Pesce wrote:
Dear All,
I am looking for available programs and/or websites able to check the
structure of DNA in DNA-protein complexes. I need to
Hi,
MBP tag:
1.there might be a TEV cleavage site in your MBP variant.
2. your protein needs salt to stay in solution
3. your protein forms aggregates with MBP
GST tag:
you probably concentrate a protease together with your protein. You need
a protease inhibitor kit to take care of different ty
Hi Pavel,
you should add to the explanation what /==1 and !=1 are, as the majority
of people don't know.
/
== : equal
!= : not equal
Maia
/
/
Pavel Afonine wrote:
Hi Regina,
this subject was discussed on PHENIX bulletin board some time ago:
http://www.phenix-online.org/pipermail/phenixbb
Could you transfer your crystals in a higher pH buffer?
Maia
Paul Lindblom wrote:
Hi,
I am trying to soak some sugars in my crystals, but the cystallization
condition has a pH of 4.0. Does anybody has any experience with acidic
oxidation in such a case. I think I can´t avoid oxidation at this
d the density of that).
Hans
Maia Cherney schreef:
Hi all,
Usually density means mass divided by volume. The mass of an electron is
known. Then it will be no arguments.
Maia
Hi all,
Usually density means mass divided by volume. The mass of an electron is
known. Then it will be no arguments.
Maia
Ian Tickle wrote:
I'm not aware that anyone has suggested the notation "rho e/Å^3".
I think you misunderstood my point, I certainly didn't mean to imply that
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