Dear colleagues,
We would like to draw your attention to this year’s call for the L*a
Caixa-Severo Ochoa International PhD Programme *at the* **Spanish National
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Dear All,
I would like to know what is the best possible way to generate the density
from the published pdb file.
thanks,
Bhat
Generate an anomalous map and look for peaks. Many metals would generate
anomalous.
On 02/04/13 07:39, Gang Dong wrote:
Dear all,
Here are some hexmeric densities we observed in our 1.6-A resolution
2Fo-Fc map. They are located in between two dimers. Although 7 waters
would fit nicely in
Hi,
I observed a very similar hexagonal arrangement of electron density blobs
in one of my structures recentely and asked the CCP4bb community to help
me explain it. Unfortunately, noone could come up with some satisfactory
explanation, so I gave up on interpreting this rogue density. What was
Frontiers in Neutron Structural Biology, Oak Ridge National Laboratory,
Spallation Neutron Source
April 16-18, 2013
This meeting will bring together scientists to discuss new opportunities for
biomedical research at the two advanced neutron user facilities (SNS and HFIR)
at the Department of
So, I know I say this every time I post on this board, but here it goes
again.
I'm at an undergrad only school, and every 2 years I teach a class in
protein crystallography. This year I'm being super ambitious, and I'm
going to take a class of 16 to the synchrotron for data collection.
Hi David
try going back to the one that started it all,* myoglobin, a recipe
is at
http://www.rigaku.com/products/protein/recipes
(* feel free to argue about this)
On 4 Feb 2013, at Mon4 Feb 16:03, David Roberts wrote:
So, I know I say this every time I post on this board, but
One more option:
phenix.fetch_pdb 1akg --maps
will fetch structure and reflection data files from PDB and generate
2mFo-DFc and mFo-DFc maps (as well as anomalous difference map if
reflection data is anomalous).
Pavel
On Mon, Feb 4, 2013 at 5:52 AM, Robbie Joosten
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Dear Gang,
By chance, P222 is your space group?
It seems to be three perpendicular two-fold axes are passing through
Dear Powell,
Isn't it there a way to data mine the PDB or the other repository source
for the time/duration/days of the crystals obtained.
Dr. Jayashankar Selvadurai
Hannover
Germany
On Mon, Feb 4, 2013 at 5:10 PM, Harry Powell ha...@mrc-lmb.cam.ac.ukwrote:
Hi David
try going back to the
I don't know. Is there?
On 4 Feb 2013, at Mon4 Feb 16:15, Jayashankar wrote:
Dear Powell,
Isn't it there a way to data mine the PDB or the other repository
source for the time/duration/days of the crystals obtained.
Dr. Jayashankar Selvadurai
Hannover
Germany
On Mon, Feb 4, 2013 at
Hi David,
You could try the Glucose Isomerase supplied by Hampton. It crystallizes
under a number of conditions, details of which you can find in their manual.
http://hamptonresearch.com/product_detail.aspx?cid=28sid=56pid=56
Ganesh
Le 04/02/13 17:03, David Roberts a écrit :
So, I know I
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Dave,
You can try any or all of these proteins commercially available and all
conditions for
crystallization and
My suggestions would be to look up citations for thaumatin and glucose
isomerase. If I remember correctly, both of them form well diffracting
crystals within a short period of time. I think you can also buy the
purified protein from a vendor. Perhaps you could also try the good old
lysozyme.
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Hash: SHA1
Dear Dave,
many methods articles mention a small set of commonly used proteins. E.g.
Mueller et al, Optimal fine phi-slicing for single-photon-counting
pixel detectors, Acta Cryst D68, p42-56 list Insulin, Lysozyme,
Thaumatin, and Thermolysin;
Nanao
Hello all,
I have recently solved a 2.0 angstrom resolution structure. The structure
is near complete but I have some unusual density at the crystallographic
interface between two chains of different asymmetric units. The linked
photos show the density at with a Fo-Fc at 3 sigma and 2Fo-Fc at 1
Bovine trypsin works well. You can buy it pretty cheap from Sigma and it
crystallizes without further purification, within a week. Crystals diffract to
1.1-1.3 A and are quite robust to handling and soaking. Conditions that I used
are described in this ref:
I second that. Gently swirling the bottle (very important) before
pipetting a few microliters (say 100 microliters or whatever).
Dialyse overnight vs 10 mM HEPES 2 mM MgCl2 ph7, then get the protein
concentration to 10 mg/ml. Set up the drops (sitting drops) versus the
same buffer with 30%
Dear Bhat,
You could use the molmap command within UCSF-Chimera (which implements the
routine pdb2mrc from the EM analysis package EMAN).
Best
Hernando
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of bhat
Sent: Monday, February 04, 2013 8:16 AM
To:
The Neutron Sciences Directorate (NScD) at Oak Ridge National Laboratory
operates the High Flux Isotope Reactor (HFIR), the United States' highest flux
reactor based neutron source, and the Spallation Neutron Source (SNS), the
world's most intense pulsed accelerator based neutron source.
Human carbonic anhdyrase II can be easily crystallized from 1.3 M sodium
citrate/0.1 M TrisCl pH 8.5 at 10 mg/mL protein concentration. Crystals
are P21 and easily diffract to beyond 2.0 A on a home source. We
cryopreserve in ML + 30% glucose. Sulfonamide ligands are easy to soak
into the
It's possibly a transition metal ion. Zinc is a common adventitious
contaminant of solutions. Typical Zn-O distances (tetrahedral or
pseudo-tetrahedral coordination) are 2.0 A. ICP-OES or ICP-MS of the
protein solution might offer a clue to the possible identity of the
metal ion, since it
On Mon, Feb 4, 2013 at 12:24 PM, Roger Rowlett rrowl...@colgate.edu wrote:
It's possibly a transition metal ion. Zinc is a common adventitious
contaminant of solutions. Typical Zn-O distances (tetrahedral or
pseudo-tetrahedral coordination) are 2.0 A. ICP-OES or ICP-MS of the protein
solution
Hi Dave,
ProteinaseK is also a good one. Crystallizes rapidly, big crystals, and
relatively high resolution data (1.0-1.5A) usually. You can also buy the
lyophilized powder from sigma and prepare the sample directly from the
commercial material. We use proK for a course here at UCLA, so if you
Hi Dave,
My experience is that students learn much better when they work
with colored proteins or crystals. Myoglobin sounds good, but I
haven't worked with it before. I worked previously with a GFP variant,
and that was challenging to grow good crystals.
Ho
Ho Leung Ng
University of
The SSRL Structural Molecular Biology Group will host a 3-day comprehensive
workshop on the use of non-crystalline small-angle x-ray scattering and
diffraction techniques in structural biology research. The workshop will focus
on solution x-ray scattering studies on biological macromolecules
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