Hello Shipra,
If you have defined the small molecule with a cif dictionary file (used for
refinement in REFMAC), then take a look at that file and see whether it is
correctly defined.
You can manually edit these files or remake them using any number of programs
to get the parameters you think a
I agree with Roger that human CAII is easy to express in E. coli at high level
and does not need a tag for purification- and that it is a good lesson for
students to purify proteins without tags (they sometimes have better activity
and crystallise better without having the tag).
It is also easy
Hello Vivek,
As Brian has mentioned, the angle is an important aspect, but most people
consider distances of 2.4 to 3.2 (although there is some variability here to go
slightly longer/ shorter, say 2.3 to 3.3) Angstrom to be a hydrogen bond
distance between two 'heavy' atoms like oxygen and nitr
Hello Gourab,
DMSO is not the only possible solvent- there are others to try.
I don't want to sound negative, but 40 micromolar is not a very tight binding
compound. It would also depend on how that binding constant was measured- how
did someone get enough in solution to measure that?
Best of lu
Hello Herman,
If you have plenty of the fusion protein, there is probably no reason not to
set it up in crystallisation trials and see if you get something.
There are published reports of proteins crystallising with fusion partners, but
I suspect there are a whole lot of unpublished results of t
Speaking of Linux, but somewhat tangential to the thread:
Ubuntu has recently released their newest version 20.04 (Focal Fossa).
Has anyone implemented this and is there anything that doesn't work? Any
gotchas that one might want to be aware of?
Cheers, tom
Tom Peat, PhD
Proteins Group
Biomedica
Although they can now get the fold correct, I don't think they have all the
side chain placement so perfect as to be able to predict the fold and how a
compound or another protein binds, so we can still do complexes. I don't know
what others end up spending their time doing, but much of my work
Hello Jon,
We had a novel structure and it did very well. I haven't tried the MR to see if
the model would work, but it was so close that I can't imagine it not working.
Our protein was ~185 residues and the closest PDB structures were about 4
Angstrom rmsd over about 70 residues over just one
Hello Murpholino,
OpenEye Scientific Software may still have a working version of the BDP, but
you would need to inquire with them.
Best of luck, tom
Tom Peat, PhD
Proteins Group
Biomedical Program, CSIRO
343 Royal Parade
Parkville, VIC, 3052
+613 9662 7304
+614 57 539 419
tom.p...@csiro.au
___
Hello Anamika,
>From the information you gave, you have two different promoters- araC and the
>lac promoter. LacI is the lac inhibitor. The lac promoter is a two part
>system- when lactose is not present, the inhibitor sits near the promoter and
>blocks transcription of genes downstream.
Almost
Hello All,
I would like to run SIMBAD to do a brute force MR on a data set that I have
(running Contra-Miner didn't come up with any known contaminants and running
SIMBAD with the Lattice and Contaminants search didn't give me anything).
As I understand the documentation, SIMBAD can be run using
agreement again…
Cheers, tom
From: bogba...@yahoo.co.uk
Sent: Wednesday, 24 June 2020 10:29 AM
To: Peat, Tom (Manufacturing, Parkville)
Cc: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] number of frames to get a full dataset?
Well, it can still help. I used to be a great fan of inverse-beam expts! Oh
I would just like to point out that for those of us who have worked too many
times with P1 or P21 that even 360 degrees will not give you 'super' anomalous
differences.
I'm not a minimalist when it comes to data- redundancy is a good thing to have.
cheers, tom
Tom Peat
Proteins Group
Biomedical
Hello Jiyuan,
One small point to note- as Artem says, small molecule crystals are often
generated out of solvents and these same solvents often melt the standard
protein crystallisation plates, so be careful what you put into a plastic plate.
As Artem mentioned, synchrotrons are generally overk
Hello All,
For some time now I've had some issues with ccp4i starting up. Specifically it
seems to be the drawing of new windows, so it happens upon starting up the main
window, any application window, etc. The window starts (a small 'icon' window
is drawn) and then things just hang. So I'm gue
There are fairly cheap adapter eye-pieces that can be purchased that will hold
most of the standard phones (iPhones 5, 6, 7, etc).
They work very well and we have replaced our old microscope camera with these
and the pictures are great (for one offs, not for taking time courses over many
drops/p
As was suggested, you can take a small drop and use pH paper to get a rough
idea of the pH.
The pH will go acidic over time as you have 20% PEG in there. This is an issue
with all PEG conditions, so your specific pH will not be known by someone
outside your lab as they don't know how old your sc
Yes, but are we poets or scientists?
Wax lyrical in your poetry, but maybe have some standards in our science?
cheers, tom
Tom Peat
Proteins Group
Biomedical Program, CSIRO
343 Royal Parade
Parkville, VIC, 3052
+613 9662 7304
+614 57 539 419
tom.p...@csiro.au
From
I will agree with Artem here-
Having knowledge as to whether crystallisation is likely or not with a given
protein/ complex would be extremely useful.
If there were a set of screens/ tests/ experiments that one could run to show
that it was 99% certain that something was not going to work (or con
Hello Tim,
I'm not sure this question is specific to crystallography- I believe the same
can be asked of any experiment in any field?
And if one wants to get into true costs- was it worth it to build the Large
Hadron Collider to statistically prove that the Higgs boson exists?
I'm guessing it
If one were able to crystallise almost all proteins (and complexes) reliably
and with good diffraction, that would make most people's lives much easier. So
I would go with 1) as a grand challenge.
Many of the rest follow on from not having 'good' crystals to start with.
cheers, tom
Tom Peat
P
reset a machine with the power button.
HTH,
Kay
On Mon, 15 Jul 2019 05:24:38 +, Peat, Tom (Manufacturing, Parkville)
wrote:
>Hello again,
>
>To be more specific- sometimes when Coot crashes, I can just restart Coot.
>Sometimes it locks my whole machine (maybe 30% of the time) an
Hello again,
To be more specific- sometimes when Coot crashes, I can just restart Coot.
Sometimes it locks my whole machine (maybe 30% of the time) and I need to
reboot.
The former is just a small pain, the latter is a true pain and I prefer
software not to crash the machine in such an untidy
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