Dear Crystallographers,
Thank you all for responding! I will try to respond to the suggestions
collectively. I did however have some questions for some of these suggestions...
@Herman Schreuder: I have performed refinement with alt conform as you
suggested. I am not sure how to do group-occupan
I just noticed that the PDB has changed the stated resolution for one of my old
structures! It was refined against a very anisotropic data set that extended
to 2.2 in the best direction only. When depositing I called the resolution 2.5
as a rough average of resolution in all 3 directions, but
Hi David
I was using a very similar Belle Technology setup during my PhD.
One thing we did was to modify the receiving dewar in the microscope chamber by
screwing in small metal clips to the inside wall such that standard Hampton
magic wands could be clipped immediately after plunging. That allo
wow this is pretty crazy you should check this out
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Thanks for all the input. I'll try to respond to some of the points made.
Kelly - the dewar is quite narrow in diameter so there's little space to
maneuver, the puck fits snugly. Unfortunately we are limited by the
size of the port so we can't use a larger one. Additionally the dewar
sits b
Think about "hyperquenching" (a high-falluting name meaning to use a stream of
gas to blow off the cold layer that accumulates above the surface of the liquid
nitrogen). We just blow some nitrogen at the surface of the dewar, very low
tech...but it works. Importantly, you can use a more leisurel
We have a similar setup at Leicester, but its new enough not to have got
that far yet!
I'd be interested in any replies you get.
best wishes, Peter
On 24 April 2012 15:20, David Gallagher wrote:
> Hi all,
>
> I've been using a Belle technologies anaerobic glovebox with in built
> microscope
Hi,
Sometimes the forming of ice is due to the high humidity in the air. I
recommend to put a dehumidifier in the room or silicone gel in your camber.
Nian
On Tue, Apr 24, 2012 at 9:52 AM, Kelly Daughtry wrote:
> Is there room in the LN2 to plunge directly in, then maneuver into
> puck? That's w
> On Tue, Apr 24, 2012 at 10:20 AM, David Gallagher
> wrote:
>> I've been using a Belle technologies anaerobic glovebox with in built
>> microscope and liquid nitrogen dewar port [...]
>> plunging loops straight into vials preloaded into an ESRF puck
why, why, why, and why?
>> [...] This requir
Naveed,
You mention:
The active site hydrophobic crown had been
reported to re-orient and a charged residue is known to position for
forming a salt-bridge with similar ligands.
When you induce structural changes on ligand binding, lattice forces that
stabilize
one particular conformation may
Is there room in the LN2 to plunge directly in, then maneuver into
puck? That's what I did, with a different setup, but still anaerobic and
moving into pucks. I did not run into ice problems. If there is not room
within the LN2 bowl, can you use a larger one?
I've found any hesitation when headin
Hi all,
I've been using a Belle technologies anaerobic glovebox with in built
microscope and liquid nitrogen dewar port in an attempt to harvest and
cryo-cool crystals in an oxygen free environment.
I've been having some problems with icing and think this is most likely
due to slow speed tha
Interesting. One of the most helpful ways of ascertaining whether you do have a
bound ligand (or, as Jay suggests, bound but modified ligand/protein) is, of
course, to compare the electron density you see in the complex with the
corresponding unliganded (let’s say apo) complex (in your case, the
http://mathworld.wolfram.com/StandardDeviation.html
On Tue, 2012-04-24 at 09:13 +0800, Qixu Cai wrote:
> Dear Ed,
>
> Why the variance is the square of standard deviation?
>
> thank you very much!
>
>
> 在 2012年4月23日，20:53，Ed Pozharski 写道：
>
> > On Sun, 2012-04-22 at 12:47 +0530, Arka Chakrab
Naveed,
From your description, it appears as if some covalent changes have occurred in
the 2 weeks of soaking. Perhaps your inhibitor is getting turned over by the
enzyme ?
Also, if you don't have your inhibitor in the cryo, you could be soaking it out
prior to data collection, which may explai
Dear Tim,
Sorry about my typo. I just want to know what is the unit of variance when
the standard deviation has the same unit as the values?
What's the definition of variance actually?
Thank you very much!
在 2012年4月24日 下午4:01，Tim Gruene 写道：
> -BEGIN PGP SIGNED MESSAGE-
> Hash: SHA1
>
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Hash: SHA1
Dear Qixu,
there is no contradiction in your quotes and what you are thinking:
* "The standard deviation has the same unit as the values you're
measuring."
* I always think that the unit of deviation is the same to the values
we're measuring.
th
Dear Naveed,
>From your description, I get the impression that indeed you have a partially
>bound inhibitor.
However, I do have some comments:
At 1.7 Å, you should refine a group-occupancy for your inhibitor.
With a partially bound inhibitor, the density in your active site will be a
superpos
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