Integrins?
Loads of structures and models .
On 24 Sep 2013 16:49, Edward A. Berry ber...@upstate.edu wrote:
Gloria Borgstahl wrote:
Hello ccp4ers,
I am helping a colleague develop a grant and have a vague recollection of
structures of
transmembrane protein receptors that signal across the
Following on from John's comment, when I did my PhD at Birkbeck in the
early 2000s, one of David Moss's other PhD students (John Bond) grew some
gigantic (1cm edges) crystals of things like HEWL Myoglobin, which he
then (somewhat perversely) crushed to load into capillaries for powder
diffraction
Hi Rhys,
It's worth paying close attention to your crystallisation conditions as
well - some heavy atom compounds will not be at all soluble in very
alkaline (they'll form insoluble hydroxides) or phosphate/sulphate
containing mother liquors.
A very low pH may reduce the binding efficiency of
Dear all,
sorry for the slightly off topic post,
I have 2 proteins that have been shown to interact, by multiple groups, and
by multiple techniques - namely ELISA, SPR and DPI.
The Kd of the interaction as determined by SPR is on the order of 1 nM.
I would very much like to crystallise this
interactions with the blank surface were seen
Thanks once again everyone,
Dave
On 21 Jan 2014 15:51, David Briggs drdavidcbri...@gmail.com wrote:
Dear all,
sorry for the slightly off topic post,
I have 2 proteins that have been shown to interact, by multiple groups,
and by multiple techniques
Hi Careina,
I'm not sure you can assume that the ratio of monomer and dimer will stay
constant through the column - as you say, the protein is diluted during the
run, the ratio will change, unless you have a super tight dimer - which
clearly you do not. Also, as the mass and the molar extinction
Hi Tom,
Are your protein or related proteins known to dimerise?
Is the dimer perhaps the natural state, and are the high oligomers
non-specific aggregation?
That would be my first guess, knowing nothing about the protein you are
working on.
If you are absolutely certain that the protein should
Integrin-ligand binding?
See for example: http://humphrieslab.info/integrins.html
Dr David C Briggs PhD
http://about.me/david_briggs
On 27 Feb 2014 19:43, Keller, Jacob kell...@janelia.hhmi.org wrote:
Dear Crystallographers,
Does anyone know of good examples of large, reversible
AFAIK, Dr Smart now works at Global phasing.
https://www.globalphasing.com/people/osmart/
HTH,
Dave
Dr David C Briggs PhD
http://about.me/david_briggs
On 12 Mar 2014 19:46, Appu kumar appu.kum...@gmail.com wrote:
Hello everyone,
I request all of you to please
Hi Faisal,
Take a look at Marjorie Harding's website
http://tanna.bch.ed.ac.uk
Loads of information there.
Hth,
Dave
Dr David C Briggs PhD
http://about.me/david_briggs
On 17 Apr 2014 21:16, Faisal Tarique faisaltari...@gmail.com wrote:
Dear all
Can anybody please explain what is the
So, a bit like Fold-it but with actual data? :-D
Dr David C Briggs PhD
http://about.me/david_briggs
On 16 May 2014 06:19, Pavel Afonine pafon...@gmail.com wrote:
What about structures that are obviously wrong based on inspection of the
density, but no one has bothered to challenge yet? The
Solubility issues though?
Dr David C Briggs PhD
http://about.me/david_briggs
On 13 Jun 2014 11:45, Ian Clifton ian.clif...@chem.ox.ac.uk wrote:
avinash singh avns.si...@gmail.com writes:
wwdwwwy
Wow, imagine the fluorescence from that…
--
Ian ◎
Hi Lionel,
A few musings/suggestions
If they are bound *inside* the protein, this suggests that the
phospholipids might be very tightly bound.
Do you have an affinity tag on your protein (e.g. His tag)? Perhaps you
might immobilise the protein on a suitable resin and wash with copious
amounts
?
Failing that - try altering the construct - add / remove a few amino acids
at each end, truncate any predicted loops...
HTH,
Dave
[image: David Briggs on about.me]
David Briggs
about.me/david_briggs
http://about.me/david_briggs
On 16 July 2014 15:55, Bishop, Catherine E. cati...@ou.edu wrote
Hi Sajid,
*Assuming* you have one site per monomer (rather than, say, one site per
dimer), and *assuming* each binding event is completely independent ( I.e
no co-operativity), you might just get away with running the experiment
with the heterogeneous material.
However, you might not be able to
Hi Xun,
it is difficult to judge without seeing the P(r) plots, but seeing as
you have a dimer in your crystal structure and a dimer in your SAXS,
AND your Chi2 value seems reasonable for a good match between PX and
SAXS, I'd say you've got what you need.
A matching P(r) plot would be nice, but
Dear Xun,
Regarding your monomer vs dimer, theoretical vs observed crysol plots
- yes - they are significantly different.
If you focus at the very lowest q part of the curve - the deviation
there in your monomer plots indicate that there is a significant size
difference between your PX monomer
Hi Vijay,
Not an answer to your question, but I tried and failed to source any
about 10 years ago. I had a chemist friend try to make some following
the a protocol we found on the web - which didn't work.
The consensus on the ccp4bb back then was that it was a bit of
mythical beast, and I never
Hello Adrian,
I use Research Gate and there are a few occasions where I have found
it useful, particularly the questions feature.
HTH,
Dave
David C. Briggs PhD
http://about.me/david_briggs
On 30 October 2012 16:13, Adrian Goldman adrian.gold...@helsinki.fi wrote:
Hi Sarathy,
Are you sure your anomalous scatterers are not the Ca in the
crystallisation buffer? These would also bind to the acidic residues in
your protein, and Ca has a greater f'' (~2.5e compared to less than 1.5e
for S) at the wavelength you used.
Just another possibility - unless you
Hi Shankar,
I don't claim to be an expert, but I've used ethylene glycol as a
cryoprotectant many times, and 30% (v/v) would probably be sufficient for
proper freezing without any further addition.
Did you try and shoot a crystal at room temperature?
Hth,
Dave
On Jan 2, 2013 5:59 PM,
Hi Sebastiano,
Phyre Alarm would do something similar to what you suggest.
http://www.sbg.bio.ic.ac.uk/phyre2/html/help.cgi?id=help/phyrealarm
HTH,
Dave
David C. Briggs PhD
http://about.me/david_briggs
On 20 March 2013 12:40, Sebastiano Pasqualato
Following on from that - readers may be interested in Stephen Curry's
post in the Guardian, regarding the Crystallography exhibit at the
London Science Museum.
http://www.guardian.co.uk/science/occams-corner/2013/apr/19/1
regards,
Dave
David C. Briggs PhD
the addition of a _reducing_ agent would _reduce_ your disulphides -
i.e. break them.
Dave
Pete
Pete Meyer
Fu Lab
BMCB grad student
Cornell University
--
---
David Briggs, PhD.
Father Crystallographer
www.dbriggs.talktalk.net
iChat AIM ID: DBassophile
Cambridge CB10 1SA
Work Tel: 0044 (0)1223 834244 ext. 7318
Cell No.: 0044 (0)7870 208280
===
Cynthia Kinsland, Ph.D.
Cornell University
Protein Facility Director
607-255-8844
--
---
David
in advance,
Dave
--
---
David Briggs, PhD.
Father Crystallographer
www.dbriggs.talktalk.net
iChat AIM ID: DBassophile
---
Anyone who is capable of getting themselves made President should on no
account be allowed to do the job
--
---
David Briggs, PhD.
Father Crystallographer
www.dbriggs.talktalk.net
iChat AIM ID: DBassophile
---
Anyone who is capable of getting themselves made President should on no
account be allowed to do the job. - Douglas Adams
in the subsequent refinement,
which one I should accept and go forward.
Thanks.
Sam
_
Discover the new Windows Vista
http://search.msn.com/results.aspx?q=windows+vistamkt=en-USform=QBRE
--
---
David Briggs
--
---
David Briggs, PhD.
Father Crystallographer
www.dbriggs.talktalk.net
iChat AIM ID: DBassophile
---
Anyone who is capable of getting themselves made President should on no
account be allowed to do the job. - Douglas Adams
. Have the authors deposited the
Structure factors? I would use EDS to check the maps out: eds.bmc.uu.se/eds/
thanks,
Ibrahim
HTH, Dave
--
---
David Briggs, PhD.
Father Crystallographer
www.dbriggs.talktalk.net
iChat AIM ID: DBassophile
--
---
David Briggs, PhD.
Father Crystallographer
www.dbriggs.talktalk.net
iChat AIM ID: DBassophile
---
Anyone who is capable of getting themselves made President should on no
account be allowed to do the job. - Douglas Adams
?
Cheers,
Dave
--
---
David Briggs, PhD.
Father Crystallographer
www.dbriggs.talktalk.net
iChat AIM ID: DBassophile
---
Anyone who is capable of getting themselves made President should on no
account be allowed to do the job
Hi everyone,
I know that this has been discussed on the bb before now, but 20 pages of
google search in, I have still come up with zip.
I want to vary b-factors smoothly from either point or a plane. This is for
pretty-picture purposes.
I can then colour molecule by b-factor and get nice, pretty
Hi Andreas,
This maybe a little ott, but the Rosetta suite of modelling programs will do
docking with some minimisation and side chain optimisation. You can also
enforce symmetry.
http://www.rosettacommons.org/
http://depts.washington.edu/bakerpg/
It is free to academics and runs on most
The review cited below is a great source of ideas to help you get your
ligand in your crystals
Hassell, A et al
Acta Crystallogr D Biol Crystallogr. 2007 Jan;63(Pt 1):72-9.
Crystallization of protein-ligand complexes.
Hopefully it may help you!
Dave
On 11/12/2007, Schubert, Carsten [PRDUS]
Whilst the joys of Facebook are fresh in our minds...
http://www.facebook.com/event.php?eid=6213885939
D
On 17/12/2007, Gerard DVD Kleywegt [EMAIL PROTECTED] wrote:
I thought that I would never have to disagree with both Eleanor and
Tassos in the same email, let alone risk being burnt at a
Covalent modification?? Bias in 2fo-fc map?
Can you show us a pic of offending density?
Dave
On 28/12/2007, Brenda Patterson [EMAIL PROTECTED] wrote:
Hello,
I am fairly new to this lark so please forgive me if this question is
unclear,
but it is really puzzling me.
I have used phaser to
I'll defend the honour of the phoenix... (again)
Bernhard Rupp 100+100 nl
Dave Briggs (and all users at Univ of Manchester, UK) 100+100nl
Others..
Only time we have ANY problems is when the nano dispensing tip gets clogged.
Often a good wash whilst still on the machine will clear the blockage.
Hello Yadong,
This is what I would do in your position.
1) Integrate everything in MOSFLM
2) Enforce consistent indexing using POINTLESS (unless I am mistaken, there
are alternative origin(s) in p321)
http://www.ccp4.ac.uk/dist/html/alternate_origins.html
Oops.
My link terminology were a little wayward...
I knew what I meant, but the incorrect link may have proven misleading.
But the answer essentially remains the same:
1) Integrate everything in MOSFLM
2) Enforce consistent indexing using POINTLESS (unless I am mistaken, there
are
Hi Chen,
You could try adding some detergent or other solubilising agent (eg
NDSBs) to your buffer.
Have you tried other pHs? If you are sat near to or on the pI of your
protein, it will be at its least soluble and more likely to aggregate.
I've had protein behave like yours at pH 7.5 but behave
Hi Jerry,
to summarise your problem, using (close to) physiological buffer, SPR
and ITC give you different results, you get different results in
different salt strengths and to add to your misery, the proteins
precipitate at low salt concentrations when mixed to together.
Ok.
Given the above,
Hi Joe,
I've known most salt crystals in Phosphate - and I think most people
are weary of phosphate.
Also, Calcium Sulphate is a fairly common one, esp if your buffers are
titrated with sulphuric acid. Fluoride Ions are also prone to form
salt crystals with transition metal ions.
HTH,
Dave
Wow, that is like, so last week(!).
I'm using COOT though a wireless interface to a head-up-display mounted
inside my contact lenses, controlled via a neural lace* embedded directly
into my parietal lobe.
I can refine and rebuild my structure whilst doing minipreps, having a
coffee, in the
Hi Sean,
You could try a scan prosite search and tell it only to search the pdb
http://www.expasy.org/tools/scanprosite/
You would enter a search pattern such as D-A-V-E and it allows you to
look for exact matches.
You can also specify to look for homologues, like [DE]-A-[VLI]-[DE]
This would
I'm not entirely sure this paper will answer your question, as I can't
access the full article at home, but I seem to remember it may contain
what you seek. It's certainly worth giving it another airing...
http://scripts.iucr.org/cgi-bin/paper?S0907444905002726
Acta Cryst. (2005). D61, 490-493
This might help...
Hassell AM, An G, Bledsoe RK, Bynum JM, Carter HL 3rd, Deng SJ, Gampe
RT, Grisard TE, Madauss KP, Nolte RT, Rocque WJ, Wang L, Weaver KL,
Williams SP, Wisely GB, Xu R, Shewchuk LM.
Abstract
Crystallization of protein-ligand complexes.
Acta Crystallogr D Biol Crystallogr. 2007
Hi Andrew
You don't say what your protein is crystallised in, or has seen during
purification, but maybe S- MERCAPTOCYSTEINE might fit?
(search for CSS in MSD CHEM)
Do you have lower wavelength data that you might get a sulphur
anomalous signal to check this?
S-methyl Cysteine might fit as well -
...by lower wavelength, I mean longer wavelength... or lower energy.
Take your pick.
Dave
2008/5/22 David Briggs [EMAIL PROTECTED]:
Hi Andrew
You don't say what your protein is crystallised in, or has seen during
purification, but maybe S- MERCAPTOCYSTEINE might fit?
(search for CSS in MSD
Morning all...
I've just downloaded the newest version of pointless, 1.2.15, using
the mac osx intel binary.
When I try and run it through the gui, it seems that my child gets hit
by some sort of bus error:
***
*
and it is
working fine - take a look at the MRC ftp site to see if you can get the
same binary:
ftp://ftp.mrc-lmb.cam.ac.uk/pub/pre
Cheers,
Graeme
-Original Message-
From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of
David Briggs
Sent: 23 May 2008 10:13
To: CCP4BB@JISCMAIL.AC.UK
as is yours -
you should be fine then. Now I think on when I asked about this a
leopard was involved, so I ended up using this.
Cheers,
Graeme
2008/5/23 David Briggs [EMAIL PROTECTED]:
Thanks Graeme,
I tried 1.2.16, and got the same problem - the most recent version I
can get to work
Hi everyone.
I have a slightly off topic question I hope someone can help with.
I have a structure of a wild type domain, which binds metal ions.
Certain mutations in chelating residues cause changes in the apparent
affinity for said metal ions.
As I have (so far) failed to crystallise the
I've used variations of the Malvern instrument at two positions now,
and I have to say I've never had a problem with them.
Yes, I believe it was designed to be a non-biological instrument, but
I have to say it does a good job of DLS and SLS on proteins from
7-200KDa (in my experience) in a
Hi y'all.
One nice cheat is to get a groovy little web server to do the work for you:
http://www.liv.ac.uk/buffers/
Enter your requirements and you'll get a nice little recipe given back.
Dave
2008/7/22 Nadir T. Mrabet [EMAIL PROTECTED]:
I bet it is more difficult to adjust a pH-meter than
Hi there,
I think 55% completeness is insufficient - you really need to collect more data.
Take a look at this movie from James Holton's website:
http://ucxray.berkeley.edu/~jamesh/movies/osc.mpeg
Stop the movie at 55% and check out how lousy the maps are compared to
95-100% - and I think
Hi Amit,
http://www.doe-mbi.ucla.edu/~sawaya/tutorials/Phasing/references.html
And the (IMHO) seminal heavy atom derivative reference:
Petsko, G.A., Perparation of Isomorphous Heavy-Atom Derivatives
Methods in Enzymology, Volume 114, , pages 147-157.
should give you all the info you need.
The
Hi Meg,
ethanol is often used in a HIC elution buffer as it is good at
breaking hydrophobic/hydrophoic interactions. (Detergents or
isopropanol can be used to do the same thing). But, as with all
things, tolerance to ethanol depends upon your protein.
At pH 5, I would guess that Citrate or
Fox GC, Shafiq M, Briggs DC, Knowles PP, Collister M, Didmon MJ,
Makrantoni V, Dickinson RJ, Hanrahan S, Totty N, Stark MJ, Keyse SM,
McDonald NQ.
Abstract
Redox-mediated substrate recognition by Sdp1 defines a new group of
tyrosine phosphatases.
Nature. 2007 May 24;447(7143):487-92. Epub 2007 May
Hi there Satheesh,
In:
Activation Mechanism of the MAP Kinase ERK2 by Dual Phosphorylation .
Cell , Volume 90 , Issue 5 , Pages 859 - 869
B . Canagarajah , A . Khokhlatchev , M . Cobb , E . Goldsmith
(PDB # 2ERK)
the structure of phosphorylated ERK II was solved by co-expressing a
suitable,
Hi there
Assuming you have a model of the complex you are interested in
tinkering with, try submitting it to the Rosetta Alanine Scanning
servery thing.
http://robetta.bakerlab.org/alascansubmit.jsp
By default, it mutates each residue in the interface to ala, does some
local minimisation (side
Hi Sheemei.
The majority of crystallography programs run under osx, including the
Uppsala software factory stuff.
Installation has always been very straight forward for me.
Bill Scott's webpages will have everything you need to get started.
http://sage.ucsc.edu/xtal/
Cheers,
David
2009/1/6
Hey - that's nothing.
For me, the first two e-mails in this thread carried a big red banner reading:
Warning: This message may not be from the alleged person or
organisation. Beware of following any links in it or of providing the
sender with any personal information. Learn more
But then - this
Jusht my two penneth...
Any list of DM programs worth a punt after MR *musht* *shurely*
include *resholve*?
Resolve ± 'primeswitch' ± NCS pretty much always comes up with the
goods for me.
Dave
2009/4/15 James Stroud xtald...@gmail.com:
Hello All,
What is the current state of the art with
Dear Jacob,
I know that this is not the answer you were seeking, but for a modest
increase in the amount of protein required, a couple of analytical
ultracentrifugation experiments would be able to determine
stoichiometry and binding affinity for such a system. AUC has the
added benefit of being
I'll add another molecular replacement anecdote to the growing list:
I like to generate some models using the Phyre server
( http://www.sbg.bio.ic.ac.uk/~phyre/ )
Feed the best .pdbs into Mr Bump.
Go and get coffee. Come back and find a solution with post-refmac
R/Rfree in the mid-30s.
IMHO,
Hammer time?
On Jul 15, 2010 4:06 PM, Badyal, Sandip K. (Dr.) sk...@leicester.ac.uk
wrote:
STOP
Hi all
I'm doing a quick talk on crystals/crystallography for a lay
audience in a couple of weeks time, and I'm looking for some time
lapse movies / animated gifs of crystal growth.
The one I was thinking of using was here:
http://microgravity.msfc.nasa.gov/snell/vibration.html
But that link is
Hi Matt,
Have you tried changing the pH? Is it possible that at pH 8 you are at
the pI of your protein (i.e. where it has zero net charge and is at
its least soluble) ?
I have also read a paper (can't find the reference right now) where
the authors precipitated their protein by dialysing into
Hi all.
I found that reference. :0)
Acta Crystallogr D Biol Crystallogr. 2006 Jul;62(Pt 7):833-42. Epub 2006 Jun 20.
Assessment of a preliminary solubility screen to improve
crystallization trials: uncoupling crystal condition searches.
Izaac A, Schall CA, Mueser TC.
Hi Xiaopeng,
There is no sign of extra density anywhere? Could the inhibitors be
binding at a site other than the active site? Is the active site
accessible from the solvent channels in the crystal?
If not, best thing I can suggest is to try and co-crystallise protein
with inhibitor - mix the
Hi Roger,
I think your ideas are sound, but I would add some prime-and-switch
density modification in resolve plus/minus ncs to try and improve the maps
and cut down on phase bias.
Hth,
Dave
--
Hand delivered by Androids
On 1 Sep 2010 16:12, Roger Rowlett rrowl...@colgate.edu wrote:
I am
Hi all.
Apologies for the off topic, largely UK-centric posting.
In a period of fiscal uncertainty in which most governments (USA,
India, China, France, Germany) are actively increasing their
investment in RD, the UK government is seriously considering cuts of
up to 25%, if press/analyst reports
I agree - looks like small molecular diffraction.
Try increasing delta-phi to catch more of the lattice to confirm - I
often do a 5º image or two with the detector pushed as close as
possible to check for salt diffraction when screening.
The lack of low res (~15-20Å) spots around the beamstop is
Rex,
the PDB statistics page at the RCSB may contain the information you seek.
http://www.rcsb.org/pdb/static.do?p=general_information/pdb_statistics/index.html
HTH,
David
David C. Briggs PhD
Father, Structural Biologist and Sceptic
Hi Greg,
I am not sure why you are so surprised! If the zinc is altering the
conformation and/or folding of your protein, this might change the
accessibility of trypsin cleavage sites, thus changing your limited
proteolysis pattern.
Eg:
Metal-ion induced conformational changes in alkaline
Hi Stefan,
It looks like a powder diffraction-type image.
http://en.wikipedia.org/wiki/Powder_diffraction
You can imagine that your spherulites are made up of many small
crystals in random orientations, a bit like a powder - this means that
rather than getting discrete diffraction spots as you
April 2011 11:29, Stefan Münnich smunn...@vub.ac.be wrote:
Hi Dave,
thanks for your reply. Is there any chance of telling whether it is salt or
protein from the diffraction image?
Stefan
On Apr 6, 2011, at 12:16 PM, David Briggs wrote:
Hi Stefan,
It looks like a powder diffraction-type
I'll give my backing to the Nanodrop as well.
I've used it in two different labs, for general yield checking use as
well as prior to ITC experiments, and haven't found there to be any
issues.
That said, I've also used cuvettes, and I find that one the whole,
cuvette-derived and nanodrop-derived
with no tryptophan
which will have a much lower extinction coefficient.
Try making a 1 g/l solution of gelatin (collagen?)
and see what its A280 is! I noticed recently the
protparam tool at http://ca.expasy.org/cgi-bin/protparam
estimates the extinction coefficient given a sequence.
David Briggs wrote
Perhaps paper and structure should be peer-reviewed independently, and only
when both have been given the green-light should both be released,
simultaneously.
I don't see why we should be especially precious about reviewing structural
data - we gladly hand functional data, protocols, etc to
Following on from Roger's fine suggestions:
8. Your column is knackered. Can you see fine lines or cracks in the
column? Good packing is v.important for SEC columns.
HTH,
Dave
David C. Briggs PhD
Father, Structural Biologist and Sceptic
the column.
Nian
On Sun, Aug 28, 2011 at 9:24 AM, David Briggs drdavidcbri...@gmail.com
wrote:
Following on from Roger's fine suggestions:
8. Your column is knackered. Can you see fine lines or cracks in the
column? Good packing is v.important for SEC columns.
HTH,
Dave
Hi Jacob,
SCAN PROSITE
http://prosite.expasy.org/scanprosite/
will do precisely what you want.
C-X-C-X-C-X-C
or
C-X-C-X-C
would be the pattern using Prosite syntax.
Cheers,
Dave
David C. Briggs PhD
Father, Structural Biologist and Sceptic
I agree with Rafael,
From those pictures it looks like a sugar chain - maybe 2-3
saccharides in a row.
HTH
D
David C. Briggs PhD
Father, Structural Biologist and Sceptic
University of Manchester E-mail:
david.c.bri...@manchester.ac.uk
Charles
I would like to echo what Keitaro suggested - can the archieves of the
talks be made available after ccp4we?
Dave
David C. Briggs PhD
Father, Structural Biologist and Sceptic
University of Manchester E-mail:
I'm pretty certain that Jalview http://www.jalview.org/ can do that
(you might have to set the user defined colours yourself).
Dave.
David C. Briggs PhD
Father, Structural Biologist and Sceptic
University of Manchester E-mail:
Hi CCP4bb,
I would like to ask about envelope phasing - specifically with SAXS data.
There are papers (1) and tutorials (2) describing how this might be
done, but I have also found comments on the ccp4bb, such as this one
(http://www.proteincrystallography.org/ccp4bb/message11690.html) which
are
in practice. Depending on the heavy atom this can
certainly help with the phase extension.
Was your question academic, or are you, like I was, stuck in low resolution
land with no phases? (I can certainly assist with the latter).
F
On Mar 12, 2012, at 2:10 PM, David Briggs wrote:
Hi
Hi Matt,
This doesn't really answer your question directly, but sidesteps
around the issue -
I wrote a little something on this exact subject not so long ago -
http://xtaldave.wordpress.com/2012/02/23/on-protein-crystallisation/
(You can ignore the first 5 paragraphs of intro - it was written
Trollus, Trollum, Trolli, Trollo, Trolli, Trollos, Trollorum, Trollis.
David C. Briggs PhD
Father, Structural Biologist and Sceptic
University of Manchester E-mail:
david.c.bri...@manchester.ac.uk
Webs :
Hi Shankar,
If you mean what I think you mean - yes, hundreds - but it depends on
how strict you are about identical'
Lots of proteins have repeat domains in them with the same fold (and
homologous sequence) and therefore very similar (if not quite
identical) tertiary structure.
Some examples
Hi Manoj,
Following on from Poul's reply, and maybe whilst you are waiting to
get derivatives ;) you could try something like the following for
getting around the model-bias-after-borderline-MR-issue.
1) generate a prime--switch'd map from resolve.
2) use this map to prune your model (be quite
Hi Hunter,
1. how to find those hydrophobic residues
PISA will also tell you this - you just need to look at the
hydrophobic residues which are highlighted and have a buried surface
area (BSA) value in the PISA output. You can take these residues and
plot them in your favourite pdb viewer
re : Paratone-N oil.
1) I find it much easier to work with if you cut it 50:50 with light
mineral oil.
2) he stress of moving mechanically weak crystals (needles or thin
plates) from a crystallisation liquor to the more viscous Paratone can
cause the crystal to visibly bend - which might not be
Just a small note of caution:
It's not a bit of vector-derived sequence is it? A bit of peptide
linker between the protein of interest and any purification tags
maybe? I know of at least one case where a piece of vector derived
sequence has been present in the crystal (and in fact been critical
This paper might provide some inspiration!
Crystallization of protein–ligand complexes
A Hassell et al
Acta Crystallogr D Biol Crystallogr
2006 vol. 63 (1) pp. 72-79
HTH,
Dave
David C. Briggs PhD
University of Manchester E-mail:
Hi Martyn,
this recipe tends to work for me...
Lysozyme: 50 mg/ml in 0.1 M Sodium Acetate pH 4.8
Reagent: 8% w/v Sodium Chloride, 0.1 M Sodium Acetate pH 4.8
Additional Reagents: Index Reagent 8, 22, 28, 31, 34, 40, 58, 59, 69, 86, 88
Mix equal amounts of lysozyme with reagent, incubate at 4 or
Hiya.
My two penneth on the Malvern Zetasizer.
Simple, idiot-proof operation. Software is easy and intuative. Reports
are customisable to give you what information you want.
Problems easy to trouble shoot IMHO.
Does DLS, SLS, melting point determination.
After-care support is good from
Sounds like you like to take a look at Art Robbins 24-4 (or is it 4-24?)
intelliplate. In the Hampton catalogue.
Hth
Dave
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Delivered via an Android.
On Feb 24, 2010 12:20 AM, Jacob Keller j-kell...@md.northwestern.edu
wrote:
Dear Crystallogrpahers,
what are the best 24-well sitting drop
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