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 and
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 Hawai
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
On Mon, Feb 4, 2013 at 12:24 PM, Roger Rowlett 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 might offer a clu
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 appea
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 cryst
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. Togethe
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: CCP4BB@JISCMAIL.AC.
A number of protein crystal recipes are available on the Rigaku web site:
http://www.rigaku.com/products/protein/recipes
Lysozyme is nice because it is so cheap, grows quickly, cryoprotectants in a
straightforward way, and the unit cells are not large nor are the crystals
fragile. One can get t
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% (v/
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:
http://www.pnas.org/content/103/18/
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
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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;
Nana
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.
Cheer
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Dave,
You can try any or all of these proteins commercially available and all
conditions for
crystallization and free
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=28&sid=56&pid=56
Ganesh
Le 04/02/13 17:03, David Roberts a écrit :
So, I know
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 5:10
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 wrote:
> Hi David
>
> try going back to the one that started it a
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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
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
wrote:
> Hi Bhat,
>
> You can
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 here
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.
It's
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 Ene
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
ce
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 Bhat,
You can run Refmac for 0-cycles to make the maps. If you use unrestrained
refinement, you don't have to mess with restraint files. There is also an
option in Coot to do this.
But if you are in Coot anyway, you might as well get the maps from EDS
directly or (after installing a plugin:
ht
Dear All,
I would like to know what is the best possible way to generate the density
from the published pdb file.
thanks,
Bhat
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
Cancer Research Centre (CNIO)**, *Madrid, Spain. The programme provides
full support for 4-years. The next deadline for applications is
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