Re: [ccp4bb] Structural transmission of signal across a membrane

2013-09-24 Thread David Briggs
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

Re: [ccp4bb] largest protein crystal ever grown?

2013-10-24 Thread David Briggs
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

Re: [ccp4bb] Best compounds for heavy atom soaks

2014-01-16 Thread David Briggs
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

[ccp4bb] Isolation of protein-protein complexes.

2014-01-21 Thread David Briggs
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

Re: [ccp4bb] Isolation of protein-protein complexes.

2014-01-21 Thread David Briggs
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

Re: [ccp4bb] KD of dimerization, off topic

2014-02-14 Thread David Briggs
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

Re: [ccp4bb] Protein behaves as dimers in 2M NaCl and as high oligomers with 300mM NaCl

2014-02-27 Thread David Briggs
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

Re: [ccp4bb] Large Conformational Change Upon Binding Ligand...

2014-03-09 Thread David Briggs
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

Re: [ccp4bb] Help in getting source of HOLE programme

2014-03-12 Thread David Briggs
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

Re: [ccp4bb] metal ion coordination

2014-04-17 Thread David Briggs
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

Re: [ccp4bb] PDB passes 100,000 structure milestone

2014-05-16 Thread David Briggs
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

Re: [ccp4bb] Www

2014-06-13 Thread David Briggs
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 ◎

Re: [ccp4bb] How to remove phospholipids bound to a cytoplasmic protein

2014-06-26 Thread David Briggs
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

Re: [ccp4bb] Salt!

2014-07-16 Thread David Briggs
? 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

Re: [ccp4bb] ITC with heterogeneous protein

2014-07-18 Thread David Briggs
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

Re: [ccp4bb] Do my SAXS data agree with the crystal structure?

2012-06-16 Thread David Briggs
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

Re: [ccp4bb] Do my SAXS data agree with the crystal structure?

2012-06-17 Thread David Briggs
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

Re: [ccp4bb] Mercury phenylglyoxal

2012-07-11 Thread David Briggs
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

Re: [ccp4bb] ResearchGate?

2012-10-30 Thread David Briggs
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:

Re: [ccp4bb] Izit dye stained crystal

2012-11-30 Thread David Briggs
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

Re: [ccp4bb] Expert opinion for optimizing ethylene glycol crystallization condition

2013-01-02 Thread David Briggs
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,

Re: [ccp4bb] PDB crawler

2013-03-20 Thread David Briggs
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

Re: [ccp4bb] popular piece on X-ray crystallography

2013-04-19 Thread David Briggs
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

Re: [ccp4bb] Fancy crystal, poor diffraction

2007-01-25 Thread David Briggs
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

Re: [ccp4bb] protease cleavage sites

2007-03-05 Thread David Briggs
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

[ccp4bb] How to get rid of Membrane formed on hanging droplets?

2007-03-05 Thread David Briggs
NIEHS, Building 101, Room F363 P.O. BOX 12233 111 T.W. Alexander Drive RTP, NC 27709 RTP, NC 27709 Tel (o): 919-316-4634 E-mail: [EMAIL PROTECTED] -- --- David Briggs, PhD. Father Crystallographer www.dbriggs.talktalk.net iChat AIM ID

[ccp4bb] Generate Random phase set.

2007-03-20 Thread David Briggs
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

[ccp4bb] Differentiating bound Mn Ca.

2007-04-16 Thread 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

Re: [ccp4bb] R and Rfree

2007-04-26 Thread David Briggs
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

Re: [ccp4bb] Second moments of Z but not twinning

2007-06-01 Thread 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

Re: [ccp4bb] B-factor Space gr questions!

2007-06-05 Thread David Briggs
. 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

Re: [ccp4bb] The importance of USING our validation tools

2007-08-30 Thread 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

[ccp4bb] Rotation Axis visualisation.

2007-09-18 Thread David Briggs
? 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

[ccp4bb] Vary b-factors from a plane/point.

2007-10-09 Thread David Briggs
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

Re: [ccp4bb] more on dimerization interface analysis

2007-11-29 Thread David Briggs
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

Re: [ccp4bb] insoluble ligand

2007-12-11 Thread David Briggs
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]

Re: [ccp4bb] WAS - Occupancy refinement... NOW - shameless promotion of facebook event.

2007-12-18 Thread David Briggs
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

Re: [ccp4bb] Difference Map in COOT - Possible lignad but clash with structure?

2007-12-28 Thread David Briggs
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

Re: [ccp4bb] crystallisation robot

2008-01-16 Thread David Briggs
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.

Re: [ccp4bb] combine incomplete data sets

2008-01-16 Thread David Briggs
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

Re: [ccp4bb] combine incomplete data sets

2008-01-18 Thread David Briggs
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

Re: [ccp4bb] protein expression problem

2008-01-21 Thread David Briggs
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

Re: [ccp4bb] salt sensitive complex

2008-01-23 Thread David Briggs
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,

Re: [ccp4bb] Characterization of common salt crystal forms?

2008-01-23 Thread David Briggs
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

Re: [ccp4bb] The Lawnmower Man

2008-03-19 Thread David Briggs
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

Re: [ccp4bb] motif search

2008-04-06 Thread David Briggs
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

Re: [ccp4bb] which concentrated salt has lowest vapour pressure?

2008-04-07 Thread David Briggs
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

Re: [ccp4bb] How to dissolve a hydrophobic peptide?

2008-04-16 Thread David Briggs
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

Re: [ccp4bb] Density Joining Cysteine and Lysine Side chains

2008-05-22 Thread David Briggs
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 -

Re: [ccp4bb] Density Joining Cysteine and Lysine Side chains

2008-05-22 Thread David Briggs
...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

[ccp4bb] Pointless Error.

2008-05-23 Thread David Briggs
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: *** *

Re: [ccp4bb] Pointless Error.

2008-05-23 Thread David Briggs
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

Re: [ccp4bb] Pointless Error.

2008-05-23 Thread David Briggs
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

Re: [ccp4bb] Protein binding to Zn and Ca

2008-06-13 Thread David Briggs
Hi there. Clostridial Alpha toxins (phospholipase Cs that cause gas gangrene) bind 2-3x Zinc in the catalytic site, and 2-3 Ca in the membrane binding domain. See 1ca1, 1olp, 1qmd and others. Dave 2008/6/13 Neeraj Kapoor [EMAIL PROTECTED]: Hi all, I recently came across a question about

[ccp4bb] Molecular Dynamics for dummies.

2008-07-03 Thread David Briggs
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

Re: [ccp4bb] DLS options?

2008-07-08 Thread David Briggs
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

Re: [ccp4bb] Na Acetate Buffer

2008-07-22 Thread David Briggs
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

Re: [ccp4bb] MR problem --molrep

2008-07-27 Thread David Briggs
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

Re: [ccp4bb] Quick-soak

2008-09-25 Thread David Briggs
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

Re: [ccp4bb] HydrophobiC interaction Chromo

2008-09-26 Thread David Briggs
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

Re: [ccp4bb] Invisible but intact disulphides?

2008-10-27 Thread David Briggs
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

Re: [ccp4bb] purification of phosphorylated proteins-off topic

2008-11-25 Thread David Briggs
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,

[ccp4bb] Fwd: [ccp4bb] site mutation evaluation

2008-12-03 Thread David Briggs
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

Re: [ccp4bb] Mac pro

2009-01-06 Thread David Briggs
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

Re: [ccp4bb] Google marks CCP4 web site as a potential security threat

2009-02-01 Thread David Briggs
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

Re: [ccp4bb] DM and MR

2009-04-15 Thread David Briggs
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

Re: [ccp4bb] Native Gel Theory and Practice

2010-05-19 Thread David Briggs
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

Re: [ccp4bb] Finding best model for molecular replacement

2010-05-23 Thread David Briggs
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,

[ccp4bb]

2010-07-15 Thread David Briggs
Hammer time? On Jul 15, 2010 4:06 PM, Badyal, Sandip K. (Dr.) sk...@leicester.ac.uk wrote: STOP

[ccp4bb] Crystal growth time lapse movies.

2010-07-21 Thread David Briggs
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

Re: [ccp4bb] Suggestions for Reducing Protein Precipitation

2010-08-12 Thread David Briggs
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

Re: [ccp4bb] Suggestions for Reducing Protein Precipitation

2010-08-12 Thread David Briggs
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.

Re: [ccp4bb] Problem with getting protein-inhibitor complex structure

2010-08-28 Thread David Briggs
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

Re: [ccp4bb] Practical MR advice

2010-09-01 Thread David Briggs
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

[ccp4bb] [OFF-TOPIC] Science is Vital.

2010-10-09 Thread David Briggs
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

Re: [ccp4bb] salt or protein crystals?

2010-12-07 Thread David Briggs
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

Re: [ccp4bb] Structures determined: breakdown of methods

2011-01-15 Thread David Briggs
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

Re: [ccp4bb] Limited proteolysis affected by metal binding?

2011-03-16 Thread David Briggs
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

Re: [ccp4bb] diffraction of spherulites

2011-04-06 Thread David Briggs
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

Re: [ccp4bb] diffraction of spherulites

2011-04-06 Thread David Briggs
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

Re: [ccp4bb] Nanodrop versus Nanophotomter Pearl versus good old Bradford.

2011-06-16 Thread David Briggs
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

Re: [ccp4bb] Nanodrop versus Nanophotomter Pearl versus good old Bradford.

2011-06-16 Thread David Briggs
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

Re: [ccp4bb] Another paper structure retracted

2011-08-11 Thread David Briggs
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

Re: [ccp4bb] Protein elution in Size Exclusion

2011-08-28 Thread David Briggs
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

Re: [ccp4bb] Protein elution in Size Exclusion

2011-08-28 Thread David Briggs
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

Re: [ccp4bb] Finding a sequence motif with BLAST

2011-10-04 Thread David Briggs
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

Re: [ccp4bb] Weird blob appears

2011-10-27 Thread David Briggs
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

Re: [ccp4bb] live streaming of ccp4 study weekend

2012-01-06 Thread David Briggs
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:

Re: [ccp4bb] off-topic: special format for multiple sequence (protein) alignment

2012-02-03 Thread David Briggs
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:

[ccp4bb] Envelope Phasing.

2012-03-12 Thread David Briggs
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

Re: [ccp4bb] Envelope Phasing.

2012-03-12 Thread David Briggs
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

Re: [ccp4bb] Unable to reproduce robot tray hits in hand trays

2012-03-26 Thread David Briggs
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

Re: [ccp4bb] very informative - Trends in Data Fabrication

2012-04-01 Thread David Briggs
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 :

Re: [ccp4bb] multi-domain protein with identical tertiary structure

2009-07-02 Thread David Briggs
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

Re: [ccp4bb] model bias

2009-08-12 Thread David Briggs
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

Re: [ccp4bb] Identification of the hydrophobic residues on the dimer interface

2009-08-19 Thread David Briggs
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: [ccp4bb] Questions about cryoprotectant

2009-10-07 Thread David Briggs
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

Re: [ccp4bb] Supplementary density

2009-10-30 Thread David Briggs
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

Re: [ccp4bb] Enzyme-Ligand complexes

2009-12-18 Thread David Briggs
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:

Re: [ccp4bb] where I have been going wrong in crystallization?

2009-12-21 Thread David Briggs
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

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