On 06/24/2011 08:50 AM, mullapudi edukondalu wrote:
Dear Members,
I have my first data set on one of my protein crystals, that diffract to
2.7 A, and the space group is I222. According to Mathews coefficient, there
should be 4 molecules in the asymmetric unit. But, when I run molecular
Well - it isnt surprising that all your geometry is good at the start.
You have fitted a refined structure against a a different crystal form,
so the first geometry report relates to your starting model which will
not be the true model which fits your new data.
Refinement has to push that
Jacob,
In case if the hint that I sent yesterday was not clear, below is the solution
for the equation
Kd=[P][L]/[PL]
in terms of ligand occupancy:
O=[ PL]/[Po]= 1/(Kd/L+1)
You see, it does not depend on [Po]
Alex
On Jun 26, 2011, at 10:05 AM, aaleshin wrote:
The concentration of a
Yes, I think you are right--the somewhat counterintuitive case I was
thinking of was, for example, when:
Kd = 20nM
[L] = 20uM
[Po in crystal] = 20mM
In this case, even though [L] = 20uM, since [L] is 1000 x Kd, the
occupancy should be ~100%, and [PL] at equilibrium should be about
20mM, so in
Hi all
Sorry for the off topic post, but given the breadth of experience on
this bb, I would like to ask.
I need to measure fluorescence from bacterial cell cultures in a
12/24/48 cell culture plate (the number of wells is unimportant). As
this is a fluorescence measurement, I require
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
Jacob,
In the formula:
Kd=[P][L]/[PL]
[P] and [L] are concentrations of UNBOUND protein and ligand, and [PL] is that
in the complex.
Since the occupancy of the ligand in the crystal is
[ PL]/[Po]= 1/(Kd/L+1),
varying [L] around Kd like from 0.1Kd to 10Kd will make the titration of
occupancy.
Hi,
You may want to have a look at the two papers below.
Experimental determination of van der waals energies in a biological system.
Wear MA, Kan D, Rabu A, Walkinshaw MD. Angew Chem Int Ed Engl.
2007;46(34):6453-6.
The First Direct Determination of a Ligand Binding Constant in Protein
A post-doctoral position is available in the group of Dr. Petri Kursula, to
study structure-function relationships in proteins specifically expressed in
the myelin sheath. The targets of the project are membrane-associated myelin
proteins, which have functions e.g. in the interactions between
Jim, that's the first thing I tried - triclinic gave similar Y-Chi2 profile.
Shiva, not sure what you mean by collecting the same crystal again (thaw and
remount?). But I collected 180 degrees, Chi2 seems to correlate with
rotation angle.
Cheers,
On Fri, Jun 24, 2011 at 1:39 PM, Jim Pflugrath
BTW, I've collected a better dataset with reasonable Chi2. Seems like the
first crystal is imperfect.
Thank everyone for your help!
On Mon, Jun 27, 2011 at 7:59 PM, bie gao gao...@gmail.com wrote:
Jim, that's the first thing I tried - triclinic gave similar Y-Chi2
profile.
Shiva, not sure
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