Re: [ccp4bb] Interesting pattern on a crystallization drop
May be, I do co-relate your crystal pic with Manu Prakash at Stanford on his
work on Dancing Droplets, briefing the surface tension and evaporation ^ the
rule of two component fluids. # Since your precipitant contain PVP a shape
controlling agent
#https://med.stanford.edu/news/all-news/2015/03/researchers-solve-mystery-of-the-dancing-droplets.html
Best wishes
S.M.Jaimohan PhD
On Thursday, 28 March, 2019, 1:54:23 pm IST, Sergei Strelkov
wrote:
#yiv3861306982 #yiv3861306982 --P{margin-top:0;margin-bottom:0;}#yiv3861306982
Artem (and Beatriz),
Me bad, could have thought about that! I think you are right.
There were initially bubbles in each drop (7 in one case, 4 in the other).
At some point the bubbles exploded (it was an instantaneous process, not just
shrinking).
Kind regards,
Sergei
Prof. Sergei V. Strelkov Laboratory for Biocrystallography Department of
Pharmaceutical Sciences, KU Leuven O&N2, Campus Gasthuisberg, Herestraat 49 bus
822, 3000 Leuven, Belgium Phone: +32 16 33 08 45, mobile: +32 486 29 41 32 Lab
pages: http://pharm.kuleuven.be/BiocrystallographyFrom: CCP4 bulletin board
on behalf of Artem Evdokimov
Sent: Thursday, March 28, 2019 1:07
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Interesting pattern on a crystallization drop Neat!
Looks like multiple adjacent bubbles that were initially touching but
eventually shrunk down to the central cores - the connectors are protein
filaments (skin on the bubbles) left over from when bubbles had contact points.
Artem
On Wed, Mar 27, 2019, 19:39 Marshall, Bevan (Manufacturing, Parkville)
wrote:
Looked up the condition on C6 (https://c6.csiro.au/C6.asp) and that condition
is found in both Index and JCSG screens as well as Classics II.
Bevan Marshall
Staff Scientist | Collaborative Crystallisation Centre
Manufacturing
CSIRO
E bevan.marsh...@csiro.aut +61 3 9662 7492
343-351 Royal Parade, Parkville, VIC 3052
www.csiro.au|https://c3.csiro.au
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From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK]On Behalf Of LEGRAND
Pierre
Sent: Thursday, 28 March 2019 9:13 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Interesting pattern on a crystallization drop
Dear Beatriz,
Nice drops :-))
Could it be that there is a reaction going on in these drops ?
The conditions are quite "exotic" with possibilities of coordination or
oxydoreduction (Co2+/Co3+) or polymerization...
Do you have reductants with the protein buffer ?
Is the protein an enzyme or a metalloprotein ?
Just some ideas.
Best wishes,
Pierre
De : CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] de la part de Beatriz Gomes
Guimaraes [beatriz.guimar...@fiocruz.br]
Envoyé : mercredi 27 mars 2019 19:44
À : CCP4BB@JISCMAIL.AC.UK
Objet : [ccp4bb] Interesting pattern on a crystallization drop
Dear all,
I would like to share with you a surprising pattern I found when examining some
crystallization plates (attached figures).
It is less obvious looking the photos, but apparently the "lines" are formed by
precipitated protein and there are some "bubbles" with small drops inside.I
wish they were microcrystals but I do not think this is the case.
I was suprised by the symmetry !
And it is not completely random because for the same condition the difference
between the two drops are : protein alone ("hexagon") and protein + ligand
("rhombus")
crystallization condition is:
0.01 M Cobalt(II) chloride hexahydrate
0.1 M Tris pH 8.5
20% w/v Polyvinylpyrrolidone K 15
Have you seen anything similar before?
Thank you for your comments!
Beatriz
--
Beatriz Guimarães
Laboratory of Structural Biology and Protein Engineering
Instituto Carlos Chagas - ICC / FIOCRUZ Paraná
Rua Prof. Algacyr Munhoz Mader, 3775 Bloco C
CIC 81350-010
Curitiba - PR, Brasil
Tel.:+55(41)3316-3225/2104-3438
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Re: [ccp4bb] AW: [ccp4bb] crystals that dont diffract :( :(
Dear Careina, Please make sure that your crystals are protein or salt, possibly using Izit dye.Note: there is no correlation so far hypothesized on the diffraction of ugly / beautiful / needle / plate type crystalsI believe! With best regardsS.M.Jaimohan PhD On Tuesday, 14 August, 2018, 7:21:09 PM IST, ferrer wrote: On 14/08/2018 12:27, Careina Edgooms wrote: Cryoprotectant was 50% PEG just added to the buffer that it crystallised in. It crystallised under batch. which kind of batch plate ? Some are not suitable to in situ. JL On Tuesday, August 14, 2018, 12:11:17 PM GMT+2, Hughes, Jon wrote: maybe it's the cryobuffer that's the problem (you didn't mention it). you could try to fish the crystals with minimal liquid attached by mounting them in oil rather than a cryobuffer. or you could test the native diffraction "in situ" (at room temperature in the drop): quite a few beamlines offer this possibility these days. best jon Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Careina Edgooms Gesendet: Dienstag, 14. August 2018 11:59 An: CCP4BB@JISCMAIL.AC.UK Betreff: [ccp4bb] crystals that dont diffract :( :( I got the most beautiful crystals I have ever seen and they don't diffract at all. Not poor diffraction, NO diffraction. Anyone know why this could be and how I can go about fixing it? I had three beautiful crystals and not one diffracted. I did leave them in the drop for about 3 weeks before harvesting and in liquid nitrogen for about a month before diffracting. Could that be a factor? If I regrew more beautiful crystals and diffracted straight away could that help? Careina To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 -- Jean-Luc Ferrer Institut de Biologie Structurale 71 Avenue des Martyrs CS 10090 38044 Grenoble Cedex 9 - FRANCE Ph.: +33 (0)4 57 42 85 22 Cell: +33 (0)6 89 45 13 57 email: jean-luc.fer...@ibs.fr To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
[ccp4bb] Separating Monomers and Dimers
Dear all,I am working on a Red FluorescentProtein (His-Tag) molecular weight around 27kDa. After purification I ran a SDSpage, the band at 27kDa confirms the monomer. The protein was stored at -20C, aweek later again I ran a gel, this time I saw another new band between 50-60kDa, it confirmsthe protein solution contains both monomers and dimers. I would like to know, whatis the best way to separate the monomers and dimers? One of my colleague adviceme to go for sucrose gradient centrifugation and size exclusion chromatography.However, I seek all your valuable suggestions and advice. With best regardsDr. S.M.Jaimohan
Re: [ccp4bb] Crystal morphology
Dear Bishwa,What about Hamptons Izit dye. S.M.Jaimohan, Ph.D On Monday, 18 May 2015 7:50 AM, Engin Özkan wrote: Magnesium phosphate crystals? I've definitely seen salt crystals with that morphology before. Check out the Ksp for Mg3(PO4)2. Engin On 5/17/15 6:45 PM, Bishwa Subedi wrote: > Hi All, > > I know that its hard to say if the crystal is protein crystal just by looking > at its morphology, however I was wondering if any of you have ever come > across protein crystals as one attached here. It would help build up my > confidence :) and work further until I put them on to X-ray beam. I could > notice similar crystals with two different proteins one in the initial screen > and one after pH screening the similar condition and involves NPS (Nitrate, > phosphate and Sulphate) from Morpheus screen. To mention, MgCl2 (0.01M) is > also added directly to the protein as a co-factor. > > Crystal condition : NPS (0.9M)+ Buffer System 2 0.1M (i.e. HEPES and MOPS) > as well as with buffer system 3 0.1M (TRIS and BICINE) at pH 7.5 and 8.5 > respectively and P550MME_P20K 30.0% > > Thank you for your opinion. > > Bishwa
Re: [ccp4bb] Offtopic: Software to closely visualize interacting partnets in protein complex
Dear Debasish,For GUI try Pymol, Chimera, CCP4MG.Also try CCP4-CONTACT not an GUI, but you get all possible interactions between two chains.best wishes S.M.Jaimohan, Ph.D On Tuesday, 10 March 2015 3:58 PM, Debasish Kumar Ghosh wrote: Dear All, Apologies for this little off-topic inquiry. I want to closely visualize the interacting residues in an multimeric protein complex to understand the nature of interactions. Is there any good software to give this information with good clarity. Any suggestion is highly appreciated. Thanks, Best !!! Debasish Kumar Ghosh CSIR- Junior Research Fellow (PhD Scholar) C/o: Dr. Akash Ranjan Computational and Functional Genomics Group Centre for DNA Fingerprinting and Diagnostics Hyderabad, INDIA Email(s): dkgh...@cdfd.org.in, dgho...@gmail.com Telephone: 0091-9088334375 (M), 0091-40-24749396 (Lab) Lab URL: http://www.cdfd.org.in/labpages/computational_functional_genomics.html
Re: [ccp4bb] Incubator for crystallization
Dear Ulrike, Molecular dimensions incubator model MD5-601 works pretty good in our lab. -Peltier type -low vibration -fully programmable up to 99 days -temperature up to 4C -accommodate low space -with RS232 Check the following links | From archives related to your question posted previously. DT2-MP-38: DigiTherm(R) 38-liter Heating/Cooling Incubator - Tritech Research, Inc. DT2-MP-38: DigiTherm(R) 38-liter Heating/Cooling Incu... View on www.tritechresearch... Preview by Yahoo EchoTherm™ IN30, IN35, IN40, IN45, IN50 and IN55 Bench Top Incubators | Torrey Pines Scientific EchoTherm™ IN30, IN35, IN40, IN45, IN50 and IN55 B... EchoTherm™ IN30, IN40 and IN50 Series Bench Top, Chilling/Heating Incubators with Fully Programmable or Non-programmable Controls Chill or heat... View on www.torreypinesscien... Preview by Yahoo Cheers Dr.S.M.Jaimohan On Tuesday, 11 November 2014 4:01 PM, Ulrike Demmer wrote: Hi everybody, I want to buy a smaller incubator for protein crystallization (30-50 l). Do you have any recommendations ? Do you prefer specialized incubator models with low vibration or are you just using standard incubators ? Best wishes, Ulrike 00,"
Re: [ccp4bb] software for powder pattern
Hi, Rigaku's PDXL software might fullfill your requirement, but I don't think its academic free. You may also try google the PDXL patch programs ICSD database | EXPO2009. Best wishes, Dr. S.M. Jaimohan On Wednesday, 20 August 2014 8:06 AM, Nancy Naguib wrote: Dear All i would like your advise about a good software for x-ray powder diffraction. i used to work on a software provided from phillips but i am not anymore. i will mainly need it for refinement for my compounds Thanks very much Nancy
[ccp4bb] EDS server - R-value
Dear all, Sorry for the off-topic Question. I just tried to extract files *.* from EDS server for a PDB entry. The page tells us that There is no map available for this entry (), because our automatic script failed to produce an electron density map with an R-value (0.309) within 5 percentage points of the published one (0.165). If you are the author of this entry and wish to help us remedy this situation, please contact us. Back to EDS home page The reported R-value for the () PDB entry is 0.16 than how 0.309? could anyone please explain about this! Sincerely, S.M. Jaimohan, Ph. D
Re: [ccp4bb] size of a flexible pdb structure
Dear Rajan, Since you raised your question about calculating the radius of your molecule. here my suggestion, a bit long back I heard about the program HYDROPRO I am not sure its going to be work for you, but you may give a try. I think the program calculates the radius of gyration ! best wishes, Dr. S. M. Jaimohan On Wednesday, 5 March 2014 8:53 PM, Tim Gruene wrote: Dear Rajan kumar choudhary, could you explain why you expect the volume to depend on the conformation of the molecule? Do you have some effective volume in mind, e.g. the elution volume during size exclusion chromatography? Regards, Tim On Wed, Mar 05, 2014 at 08:42:21PM +0530, rajan kumar wrote: > Dear all, > > sorry for asking an off topic question. My protein is composed of two > domains connected by a flexible linker (15aa). after 50ns simulation i came > across the fact that one domain is flexible. so my question is that how > could i be able to calculate the size of molecule or radius of my molecule > and which conformation i should prefer to calculate the size of molecule. > your any suggestion will be very helpful. > thank you all in advance > > with best regards > -- > *Rajan kumar choudhary* > *Senior Research Fellow* > *Department of Atomic Energy(Govt.Of India)* > *ACTREC TATA Memorial Center * > *Kharghar Navi-Mumbai* > *Mumbai-410210* > *India* -- -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A
Re: [ccp4bb] high Rwork / Rfree after MR
Dear Shanti Pal Gangwar, You are trying to solve your crystal structure of what! whether its a peptide or protein or enzyme or nucleic acid? There are several reasons behind getting a high Rmerge, it not only depends on the data quality. What are all the efforts! that you have applied to solved your crystal structure. Provide some more information like, -atleast some preliminary info of data collection methods -the program(s) you tried to process your data set -space group/unit cell length/completeness for the low and high resolution shells/ I\s. -whether your molecule is a monomer/dimer/..in asymmetric unit -have you access the data quality (very easy in Xtriage-PHENIX), whether it contains any twinning / translational pseudosymmetry. -some info about your molecular replacement programs(s) output like correlation coefficient, Rfactor | LLG, RF, TF, PAK | -the refinement program(s) you tried -hows your electron density map look like after the initial rounds of refinement you could easily include all the above information within a two or maximum three lines. If your question is very clear than definitely you will get more inputs from the experts, so that you will be guided in a right way to get your crystal structure ASAP! Regards, Dr. S. M. Jaimohan On Tuesday, 4 February 2014 8:18 PM, Bernhard Rupp wrote: …the slash at the end is obviously the secret sign for “google-translate into a randomly picked language” http://scripts.iucr.org/cgi-bin/citedin?dz5235 From:Rick Lewis [mailto:r.le...@ncl.ac.uk] Sent: Dienstag, 4. Februar 2014 15:24 To: b...@hofkristallamt.org Subject: Re: [ccp4bb] high Rwork / Rfree after MR a third of nothing is till nothing... see attached screendump ;-) On 04/02/14 14:19, Bernhard Rupp wrote: EDSTATS is part of CCP4 > >….which in fact I cite in 33% of all of its CrossRef references > >http://scripts.iucr.org/cgi-bin/citedin?dz5235/ > >Touché. > >From:CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Frank von >Delft >Sent: Dienstag, 4. Februar 2014 14:40 >To: CCP4BB@JISCMAIL.AC.UK >Subject: Re: [ccp4bb] high Rwork / Rfree after MR > >And really we should not be using real space CC or real space R anymore - not >since Tickle 2012 (http://scripts.iucr.org/cgi-bin/paper?S0907444911035918) > >EDSTATS is part of CCP4. > >phx > > > > > >On 04/02/2014 13:31, Bernhard Rupp wrote: >> interpretable electron density map is obtained to which most of your protein >> model can be fitted properly. The primary numeric indication for that are >> your R-factors. >> >>Minor comment: The measure for the fit of the *model (density) to the >>electron density* is actually a local real space correlation coefficient or a >>local real space R value, not the global reciprocal space R-values (not a >>*factor* in the mathematical sense, nor a factor for anything else). The >>overall linear residual between model structure factor amplitudes Fc and >>observed amplitudes Fo (aka R(F)-value) is a global reciprocal space measure, >>which can be affected by many other contributions causing the misfit between >>Fo and Fc data, in addition to bad model, as already noted below. >> >>Ø The high values you have suggest that either something is wrong with your >>space group, twinning, etc. as Eleanor suggested, or your space group and MR >>solution may be still correct but for a search model of poor similarity with >>your crystal structure. Even in the later case, at this resolution it is >>going to be very challenging to build and refine a structure to reasonable >>R-factors starting from a poor model. >> >>Hay >> >> >> >>Hay Dvir Ph. D. >>Head Technion Center for Structural Biology >>Technion Haifa 323, Israel >>Tel: +(972)-77-887-1901 >>Fax: +(972)-77-887-1935 >>E-mail hd...@technion.ac.il >>Website http://tcsb.technion.ac.il/Hay-Dvir >> >> >> >> >> >>On Feb 4, 2014, at 11:36 AM, Shanti Pal Gangwar wrote: >> >> >> >> >> >>Dear All >>I have solved one structure by MR. The data data quality was poor so the >>Rmerge was high. The resolution of the data is 3.3 Angstrom.The refinement >>statistics are also very poor Rw/Rf= 40/42 %. After many efforts we are not >>able to get reasonable Rw/Rf. >> >>My question is "can it be claimed that we have solved the structure?" >> >> >> >> >>Thanks in advance >> >> >> >> >> >>-- >> >>regards >>Shanti Pal Gangwar >>School of Life Sciences >>Jawaharlal Nehru University >>New Delhi-110067 >>India >>Email:gangwar...@gmail.com >> >> >> >> >> > -- R. J. Lewis Professor of Structural Biology Institute for Cell and Molecular Biosciences Faculty of Medical Sciences Tel: +44 (0)191 222 5482 University of Newcastle Fax: +44 (0)191 222 7424 Newcastle upon Tyne, NE2 4HH,
Re: [ccp4bb] 'ERROR' in merging two data sets
To Eleanor, I changed the column label for two data sets, FreeR_Flag for the first data and F_x for the second data. Now CAD compiled the data successfully. The merged MTZ file contains column label like this H K L FreeR_Flag F_x I conclude to use this file for molecular replecement or / i need to use any other program to generate the final file. I am sorry about my silly question because this is the first time that i am working in two data sets. (unfortunately the data set found to be isomorphous). regards Jaimohan S.M. --- On Thu, 30/9/10, Eleanor Dodson wrote: From: Eleanor Dodson Subject: Re: [ccp4bb] 'ERROR' in merging two data sets To: CCP4BB@JISCMAIL.AC.UK Date: Thursday, 30 September, 2010, 2:36 PM Different numbers of columns wont stop CAD working, but if you have the any occurence of the same labels in either file this will produce an error mesage - eg Label FreeRflag found twice.. And if you have labelled both data sets as Fnew or some such uninformative label, then again you will have this problem. However maybe as Phil suggests you dont want a file with H K L F2.0 etc F1.9Etc But you really want to merge the two sets of measurements into a single data set? Eleanor jai mohan wrote: > > Dear all crystallographers, Recently I have collected two data sets from two > different crystals, first data at 2.6A and second is at 1.9A, the datasets > were isomorphous. I tried to merge the two dataset as a single MTZ file > using CAD (CCP4i), but it is unsuccessful, i hope that the error starts from > the column label of the data sets. The first data has 13 and second data has > 18 columns. Please guide me how do i select the column labels. Need all of > your valuable suggestion and advice. > regards > Jai > > >
[ccp4bb] 'ERROR' in merging two data sets
Dear all crystallographers, Recently I have collected two data sets from two different crystals, first data at 2.6A and second is at 1.9A, the datasets were isomorphous. I tried to merge the two dataset as a single MTZ file using CAD (CCP4i), but it is unsuccessful, i hope that the error starts from the column label of the data sets. The first data has 13 and second data has 18 columns. Please guide me how do i select the column labels. Need all of your valuable suggestion and advice. regards Jai
[ccp4bb]
Dear Askok, There is many programs & online servers to do this task, i prefer you profit server, http://www.bioinf.org.uk/profit/ best regards jaimohan --- On Sat, 24/10/09, ashok kumar wrote: From: ashok kumar Subject: [ccp4bb] To: CCP4BB@JISCMAIL.AC.UK Date: Saturday, 24 October, 2009, 6:07 PM Dear all i want to know is there any programme to calculate the r.m.s deviation of a some segment while superimposing the whole molecule together. Thanks in advance for any suggestion Ashok Now, send attachments up to 25MB with Yahoo! India Mail. Learn how. http://in.overview.mail.yahoo.com/photos
Re: [ccp4bb] Regarding BMCD
Dear Nishant, You may follw this link below, after you indicate the protein/enzyme/nucleic acid name don't hit ENTER [probably it wont work] CLICK submit. http://xpdb.nist.gov:8060/BMCD4/index.faces;jsessionid=b196fdf1b356c8293b85a9f3981d jaimohan --- On Fri, 12/6/09, Nishant Varshney wrote: From: Nishant Varshney Subject: [ccp4bb] Regarding BMCD To: Date: Friday, 12 June, 2009, 12:38 PM Dear all, I have bee trying to access the biomolecular crystallization database BMCD for quite sometime now, no matter which route I access it through the page shows an error as the server can not be contacted. I would like to know whether its a problem only I am coming across.Moreover, is there any registration or license required to access BMCD? if there is, I am not aware of it. Your help will be appreciated. Regards Nishant NISHANT KUMAR VARSHNEY C/O Dr. C.G. Suresh, Biochemical Sciences Division, National Chemical Laboratory, Pune-411008, Maharastra, India. Share files, take polls, and make new friends - all under one roof. Click here. Own a website.Get an unlimited package.Pay next to nothing.*Go to http://in.business.yahoo.com/
