Hi Liew,
Have you ever tried paratone or some other oil?
Sincerely,
Li
__
Email:s...@sibs.ac.cn
Institute of Biochemistry and Cell Biology
Institutes for Biological Sciences
Chinese Academy of Sciences
320 Yue-Yang Road, Shanghai 2
Hi all,
Good day
I used MPD as a cryoprotectant (20%, 30%) for my crystal. However, there is no
diffraction signal at all. Without the MPD cryo, i still manage to get
5angstrom, but it has very strong ice-ring signal. I used glycerol (15%, 20%,
25% and 30%) before, but it cracked the crystal.
Dear Li,
In regards to concentration ideally you should do a concentration series
and from that perform a zero concentration extrapolation. Typically we've
had success with a 1-10 mg/ml series and 1.5-3 s exposures at SSRL but
it's going to be dependent on molecular weight. You should monitor your
Dirk Kostrewa wrote:
yes, this is certainly true for real fluorescence effects. But the
anomalous scattering can be best thought of as a resonance phenomenon
without any frequency change, and as such, it has a distinct phase
relationship to the elastically scattered photon and does have an
eff
Hi Francis,
The asymmetric unit volume is approximately proportional to the number
of atoms in your model, the basis for Vm, with some variation due to
solvent content. In turn the number of unique observations at a given
resolution is proportional to asymmetric unit volume. So twice the
numb
Since the SAXS signal comes from the size of your scattering
particles, make sure you don't have large non-protein particles in
your sample (dust or micelles, for example). The SIBYLS web site has
additional warnings about including detergents in your sample.
ho
UC Berkeley
Francis,
of course don't know about your sequence, but one normally uses 7-8 atoms
(non-H) per residue...so I tend to think you'll end up with <3000
parameters (of course if you decide to refine individual B-factors, which
would typically make sense for a 2.0A res data set...)
(and then of cou
On Thu, Apr 23, 2009 at 2:54 PM, Francis E Reyes wrote:
> It seems I have a case where I have 5595 reflections but my protein is
> about 102 residues. With a mean atom / residue * 4 parameters for each atom
> I get about 7833 parameters. So it seems that I have a observation :
> parameter ratio
Use less parameters:
- TLS or group iso ADP with one-two ADP per residue (or better both, as
available in phenix.refine);
- torsion angle space instead of individual xyz;
...
Pavel.
On 4/23/09 2:54 PM, Francis E Reyes wrote:
All
It seems I have a case where I have 5595 reflections but my p
All
It seems I have a case where I have 5595 reflections but my protein is
about 102 residues. With a mean atom / residue * 4 parameters for
each atom I get about 7833 parameters. So it seems that I have a
observation : parameter ratio < 1. There is only 1 molecular per asu
so there's no
Hello All,
Bob Cudney sent me the email below (forwarded with permission), in which
good instructions are given for the pHing process. Use it in good health.
JPK
***
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
Dallos
Jacob--
We pH'd Jeffamines with concentrated HCl in the hood, but I do not recall
how much HCl we had to add to get to neutral pH. Nasty stuff. You might
want to contact Bob Cudney at Hampton Research for details since they sell
these reagents.
HTH!
annie
Annie Hassell
Glaxo Smithkline
For those who are still following this discussion...
Following a comment by James, I clarify my previous statement about
"the limiting case when the total mass of the crystal is very large
with respect to the mass of one photon"
I meant of course the "relativistic mass" of one photon [which i
Look at the moment plots after scalepack2mtz; if these are normal it
seems very unlikely you have twinning..
Eleanor
Kumar wrote:
Hi,
I am trying to solve a protein-RNA complex structure - space group is either
P4(1)22 or P4(3)22. Even though data seems to have enough Se-anomalous
signal, we
Dear Li,
The SIBYLS Beamline web page has useful sample prep information at
http://bl1231.als.lbl.gov/saxs_protocols/index.php. They also have a link
to a very good SAXS review article.
Cheers,
Angela
Li Sheng
Sent by: CCP4 bulletin board
04/23/2009 06:19 AM
Please respond to
Li Sheng
Dear Li,
as pointed out by Marjolein the sample must be MONODISPERSE, rather than
just pure. This means it should be checked not only by SDS-PAGE but at
least by size exclusion chromatography, and be sure that monodispersity
is maintained till the moment of measurements.
I guess your plans ar
James Holton wrote:
marc.schi...@epfl.ch wrote:
The elastically scattered photons (which make up the Bragg peaks) also
do not not retain the momentum of the incident photon.
Although technically true to say that photons traveling in different
directions have different momenta, all ela
Dear Li,
the samples should be devoid of aggregates, at least for the low
concentration samples. Some aggregation can be tolerated at the higher
concentrations. You should in principle measure samples with different
concentrations, such as 1, 2, 5,10 mg/mL.
The high concentration measurements w
If you go to this web-page:
http://www.embl-hamburg.de/ExternalInfo/Research/Sax/user_info.html there is
ashort summary of the requirements for a SAXS experiment. Shortly the sample
needs to be monodisperse (>90%) and you will need a range of concentrations
roughly from 0.5/1.0mg/ml to 10mg/ml
Dear all,
Is there anyone with experience in small angle x-ray scattering? Could
anyone please tell me the requirements for protein sample purity and
concentration?
Thanx in advance.
Sincerely,
Li
__
Email:s...@sibs.ac.cn
Institute of Biochemistry and Ce
S. Thiyagarajan wrote:
Dear CCP4 users
Is there any easy way of calculating the peak height / number of
electrons at a given position, say a mouse click point in coot.
Is there any formula to calculate the number of electrons based on sigma
level and peak height, as given in difference map p
Am 23.04.2009 um 02:31 schrieb James Holton:
Fluorescent x-rays have a VERY different wavelength from the
incident beam and therefore cannot interact coherently with Bragg-
scattered photons, so they contribute to nothing but background.
Fluorescence is also a true absorption-reemission pro
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