Re: [ccp4bb] Help crystalizing protein

2025-01-09 Thread Artem Evdokimov
a few emails :) Artem On Thu, Jan 9, 2025, 20:50 Marco Bravo wrote: > Hi Artem! > Thank you for the suggestions, do you have recommendation of common > protein-DNA crosslinking methods for crystalization? I suppose I also > Identified de-stablizing buffers with my thermal shift assa

Re: [ccp4bb] Help please

2025-01-09 Thread Artem Evdokimov
https://pmc.ncbi.nlm.nih.gov/articles/PMC3901029/ One that comes to mind... not sure if this is what you are looking for. Artem On Thu, Jan 9, 2025, 20:23 Chandra Verma < 64fcc5b1f9c3-dmarc-requ...@jiscmail.ac.uk> wrote: > ARES PRIVATE > > Are there examples where anyone h

Re: [ccp4bb] Help crystalizing protein

2025-01-09 Thread Artem Evdokimov
#3, or perhaps the flying spaghetti monster; all these options should work equally well. There are dozens of possible options and it is hard to say what might work for you specifically without more details. Artem On Thu, Jan 9, 2025, 20:01 Marco Bravo < d0eb7bee83ae-dmarc-requ...@jis

Re: [ccp4bb] SUMO and SUMO protease

2024-12-12 Thread Artem Evdokimov
mutations in the protease, such that the native protease does not cleave any more. Happy to help further via PM. Artem On Thu, Dec 12, 2024, 11:36 Gloria Borgstahl wrote: > Hello friends, Yet another kinda off topic question from me. I am looking > into SUMO tags for my protein of inter

Re: [ccp4bb] [OFF-TOPIC] Dissolving DMPC/ Na Cholate in buffer for nanodisc assembly

2024-12-02 Thread Artem Evdokimov
want to check is the purity of your reagents, especially DMPC - I've encountered batch issues with some of the ahem... *more affordable* suppliers in the past. Sometimes being a cheapskate is a bad thing. Artem - Cosmic Cats approve of this message On Mon, Dec 2, 2024 at 11:56 AM Rafael Marques wr

Re: [ccp4bb] Pipetting Robot

2024-12-02 Thread Artem Evdokimov
ek or so). Last time i bought one, it was reasonably budget friendly (Oryx may be still more affordable, I am not sure to be honest). Artem On Mon, Dec 2, 2024, 08:35 Sarah Bowman < ad1e26f054b6-dmarc-requ...@jiscmail.ac.uk> wrote: > We use the Formulator from Formulatrix for mixing

Re: [ccp4bb] About dry dewars

2024-10-18 Thread Artem Evdokimov
Some have a 'nipple' style valve, others have a needle style valve and some are permanently welded shut... it's not obvious that your mechanics shop will have the requisite vacuum connector to service your shipper. We used to send ours to manufacturer for reconditioning. Best of luck,

Re: [ccp4bb] Co-Crystallization with drug molecule

2024-10-02 Thread Artem Evdokimov
ystallization, needless to say. Best of luck in your endeavors! Artem - Cosmic Cats approve of this message On Wed, Oct 2, 2024 at 2:51 PM amit gaur wrote: > Hi everyone, > > I am trying to crystallize a protein with a drug molecule. The protein > concentration is 15.5 mg/ml, the

Re: [ccp4bb] Terminating a protein:cmpd covalent adduction using DTT

2024-08-27 Thread Artem Evdokimov
your outcome somehow (e.g. by small molecule MS). It's not like this reaction is hard to set up, or requires massive optimization of conditions - generally speaking, as long as you have 'much more' of DTT or BME than you have of the covalent agent, given some time the reaction w

Re: [ccp4bb] Off topic - fluorescence plate reader in cold room or cold box

2024-07-26 Thread Artem Evdokimov
ed silica gel beads in a clean sock should do the trick. With warmest regards, Artem On Fri, Jul 26, 2024 at 11:09 AM Markus Seeliger wrote: > Dear All, > apologies for the off-topic question. I am facing the problem of running > enzyme activity assays at low temperature (close to 4C woul

Re: [ccp4bb] minor off topic protein symmetry

2024-06-29 Thread Artem Evdokimov
displays one of the cutest symmetry transitions that I've seen so far. Artem - Cosmic Cats approve of this message On Thu, Jun 27, 2024 at 8:46 AM Andrew Lovering wrote: > Dear wise list, > > > > I have a question regarding protein oligomers that have multiple, > dif

Re: [ccp4bb] Ligand identification in X-ray density

2024-06-05 Thread Artem Evdokimov
At this resolution you should be able to infer differences between C and O based on the map levels at each location. Another dead giveaway is the bond lengths and the asymmetry of the top region - that is not a carboxylic acid to me. This looks lime MPD to me, very classic shape. Artem On Wed

Re: [ccp4bb] Skimming crystal

2024-05-30 Thread Artem Evdokimov
the better) and performing harvest in a cold room 5. flooding the drop with cryo (20-25% ethylene glycol is my #1 choice, but you need multiple drops to play around with different cryos of course) Best of luck! Artem - Cosmic Cats approve of this message On Thu, May 30, 2024 at 7:26 AM 白雪慧 wro

Re: [ccp4bb] Difficult Molecular replacement

2024-02-20 Thread Artem Evdokimov
where you absolutely have to treat domains as separately mobile rigid bodies. I would love to help more but it would require more sharing that you might be justifiably unwilling or unable to do :) Best of luck, Artem On Mon, Feb 19, 2024 at 6:51 PM Artem Evdokimov wrote: > Hello Ma

Re: [ccp4bb] Difficult Molecular replacement

2024-02-19 Thread Artem Evdokimov
, HRDC, etc.) Hope this helps. Artem On Mon, Feb 19, 2024, 5:54 PM Marco Bravo wrote: > Hello all, > I recently collected data on some plate crystals for a previously > uncharacterized protein at the ALS light source. The XDS auto-data > processing log output indicates that my r

Re: [ccp4bb] Äktaxpress uninet connector : Off topic

2024-02-10 Thread Artem Evdokimov
Ebay to the rescue: https://www.ebay.com/itm/185248167872 is this the correct connector? Once you have a single connector, you can pin-trace it to your hearts' delight and make new ones for pennies, since the cable and the plugs are standard... Artem - Cosmic Cats approve of this message

Re: [ccp4bb] What could these crystals be?

2023-11-08 Thread Artem Evdokimov
Could be dna crystals. They often do not diffract. Artem On Wed, Nov 8, 2023, 11:18 AM careinaedgo...@yahoo.com < 02531c126adf-dmarc-requ...@jiscmail.ac.uk> wrote: > > The reservior solution is 0.2 M NaCl2, 0.1 M HEPES pH 7.5, and 25% 3350 PEG > > Protein buffer is 300 mM

Re: [ccp4bb] What could these crystals be?

2023-11-08 Thread Artem Evdokimov
n like lattice. Of course this requires hands on access to a diffractometer, which these days isn't a common thing. All the best, Artem - Cosmic Cats approve of this message On Wed, Nov 8, 2023 at 10:02 AM careinaedgo...@yahoo.com < 02531c126adf-dmarc-requ...@jiscmail.ac.uk>

Re: [ccp4bb] [OFF TOPIC] On Ni-NTA resin TEV cleavage

2023-11-01 Thread Artem Evdokimov
speaking, resin affinity is only about 1 uM, but avidity and intra resin exchange and recapture keep the bulk of protein trapped in the resin). Good luck! Artem On Tue, Oct 31, 2023, 3:21 PM Rafael Marques wrote: > Hi everyone, > > I have been looking on this bb and other websites as well bu

Re: [ccp4bb] Autoinduction Medium

2023-10-02 Thread Artem Evdokimov
a Sci. one above) because sugars in the medium react with amino acids resulting in Brown Evil. Look it up if you're curious... In recognition of the original author, references to Studier papers: 2005: https://pubmed.ncbi.nlm.nih.gov/15915565/ 2014: https://pubmed.ncbi.nlm.nih.gov/2

Re: [ccp4bb] Autoinduction Medium

2023-10-02 Thread Artem Evdokimov
Dear Jinhui Dong You can simply make swimming-pool size amounts of it, as long as you have basic lab equipment and supplies including an autoclave, and access to ~8 chemicals. The recipe is in the Studier papers, but I am happy to share it with you here if you prefer. Artem - Cosmic Cats

Re: [ccp4bb] Adding metal ions

2023-06-16 Thread Artem Evdokimov
Take a protein structure with waters, replace surface waters with Cu++ and run some very basic MD to optimize distances. Many of the atoms will move since Cu++ will find itself in an 'unfriendly' environment, as always caveat emptor :) Artem - Cosmic Cats approve of this message On F

Re: [ccp4bb] Regarding the diffraction image

2023-02-03 Thread Artem Evdokimov
With 50 mM Zn++ in solution, whatever it is will probably have a Zn salt in it. So if you wanted to solve it by direct methods or via SAD - that should do well. Sadly (hur hur) it's probably quite small, whatever it is. Artem - Cosmic Cats approve of this message On Fri, Feb 3, 2023 at 6:

Re: [ccp4bb] small scale -15C chiller

2023-02-03 Thread Artem Evdokimov
ce, like a signal on a CAN bus or god knows what else. All the best, Artem - Cosmic Cats approve of this message On Fri, Feb 3, 2023 at 2:16 AM Tim Gruene wrote: > Hi Artem, > > the simulator is exactly what I was looking for - many thanks! > We did build a small circuit to generate

Re: [ccp4bb] small scale -15C chiller

2023-02-02 Thread Artem Evdokimov
purchase a thermocouple simulator https://www.brightwinelectronics.com/product/temperature-calibrator-k-n-thermocouple-generator-simulator Artem On Thu, Feb 2, 2023, 3:42 PM Rajkovic, Ivan < 95c2dc0d4fa4-dmarc-requ...@jiscmail.ac.uk> wrote: > Hi Tim, > > Not sure if this woul

Re: [ccp4bb] Alternative server for: Surface Entropy Reduction prediction (SERp)

2023-01-20 Thread Artem Evdokimov
Hi Yong Tang, I am not sure if there is another SER server out there, but if you can share the sequence in a private email I can run it through my code that does a similar type of analysis (it's not user friendly so I never did the right thing and put it up as a server). All the best,

Re: [ccp4bb] TEV vs HRV3C

2022-12-09 Thread Artem Evdokimov
One final comment: if you need orthogonal proteases, TEV and TVMV do not seem to cut each others' sites (at least for me they don't). No idea if 3C will cut both, or only TEV site. Artem - Cosmic Cats approve of this message On Thu, Dec 8, 2022 at 5:26 AM Dom Bellini - MRC LMB <

[ccp4bb] Deadline for LCLS screening proposals extended to Oct 4th

2022-09-30 Thread Artem Lyubimov
Hi everyone, The deadline to submit a screening proposal to the LCLS XFEL has been extended! For delicate crystals and/or for crystals available in lower quantities, the standard goniometer setup at LCLS-MFX is a useful option available to all general users applying for beamtime. See below for m

[ccp4bb] hiring (off-topic but could be of interest)

2022-08-31 Thread Artem Evdokimov
Dear CCP4-ers, We're hiring :) In case you're interested, please visit the link below. http://careers.animol-discovery.com/apply/fUyc5HcbL0/Head-Of-Medicinal-Chemistry?referrer=2022083118532124ZTDOKKYYDQHFBP Artem VP@ Animol Cheesecake

[ccp4bb] help request (synchrotron schedules)

2022-05-02 Thread Artem Evdokimov
g? If enough people share (even individual schedules) I am happy to post the resulting schedule back here for everyone to enjoy... Many thanks! Artem - Cosmic Cats approve of this message To unsubscribe from the CCP4BB

Re: [ccp4bb] Off topic - gene toxic for expression strains

2022-04-04 Thread Artem Evdokimov
ntisense. Good luck! Artem P.S. if you use 2% glucose in the media be prepared to fight acidification and the accumulation of Acetate in the spent medium, both of which can be a problem - sometimes severe - for 'weaker' E. coli strains. Strongly buffered medium is a must. - Cosmic Cats ap

Re: [ccp4bb] Strategies for increasing Trp content of proteins

2022-02-19 Thread Artem Evdokimov
Yes we chose the sites based on predicted or known structure, to be sure. No that was not a published thing, curse of commercial work :( Happy to help on a private channel. Artem On Sat, Feb 19, 2022, 1:42 PM Tanner, John J. wrote: > Casper: You make a good point about using 205 nm. I chec

Re: [ccp4bb] Strategies for increasing Trp content of proteins

2022-02-18 Thread Artem Evdokimov
many other options but their application is best considered with more information in hand Artem On Fri, Feb 18, 2022, 8:02 PM Tanner, John J. wrote: > Dear CCP4BB, > > We are working on a protein that has no Trp residues, which makes > chromatography challenging due to the low absor

Re: [ccp4bb] Baculovirus expression system

2022-02-07 Thread Artem Evdokimov
week only. As to yield - it is very protein specific and you do get many variables in play including promoters, cell lines, media additives and so on Artem On Mon, Feb 7, 2022, 11:25 AM Srivastava, Dhiraj < dhiraj-srivast...@uiowa.edu> wrote: > Hi All > sorry for the question

Re: [ccp4bb] OFF_TOPIC: Should you be worried about BPA from plastics? Yes, if you store alkaline reagents in polycarbonate bottles!

2022-01-31 Thread Artem Evdokimov
specially if one requires near-complete passivity towards strongly alkaline solutions. Artem - Cosmic Cats approve of this message On Sun, Jan 30, 2022 at 1:02 PM Edward Berry wrote: > After using the same reagents for the Lowry assay and seeing the color > yield in the standard curve gradua

[ccp4bb] multiple openings in my team @ Roivant

2021-12-13 Thread Artem Evdokimov
ector, Biochemistry https://www.roivantcareers.com/job/associate-director-biochemistry-research-development-us-ma-boston-451-d-street-33-2057292/ Artem, the washer of many bottles (and also VP of biochem/biophys/structure and hit finding) - Cosmic Cats approve of this me

[ccp4bb] (off topic) Job posting - Associate Director, Protein Science

2021-10-19 Thread Artem Evdokimov
https://boards.greenhouse.io/roivantsciences/jobs/3549863 Finally posted! Thank you for looking. Artem - Cosmic Cats approve of this message To unsubscribe from the CCP4BB list, click the following link: https

[ccp4bb] job opening: Associate Director, Protein Sciences

2021-10-08 Thread Artem Evdokimov
, sex, national origin, disability status, genetics, protected veteran status, sexual orientation, gender identity or expression, or any other characteristic protected by federal, state or local laws. Thank you, Artem (VP of stuff @ Ro

[ccp4bb] Research Associate position at SSRL-SMB

2021-07-30 Thread Artem Lyubimov
The Structural Molecular Biology (SMB) Division at the Stanford Synchrotron Radiation Lightsource (SSRL) is seeking a Research Associate with a strong background in X-ray diffraction data processing and/or software development. A successful candidate will work with an interdisciplinary group of cry

Re: [ccp4bb] RNA-PROTEIN purification on FPLC

2021-06-21 Thread Artem Evdokimov
purify your material. If your RNA is single stranded, it will have a hard time surviving this ordeal. Of it is double stranded, should be no worries. Artem On Mon, Jun 21, 2021, 8:47 PM WENHE ZHONG wrote: > Dear members, > > We are planing to purify RNA only or/and RNA-protein comple

Re: [ccp4bb] Enzyme Vmax and Km

2021-06-18 Thread Artem Evdokimov
y when you add more substrate than enzyme the monomers of enzyme can become 'smeared' along the DNA and this results in very odd kinetic behavior. Artem On Fri, Jun 18, 2021, 12:05 AM Prem Prakash wrote: > Dear all, > Sorry for this off topic. I am working on an enzyme that has

Re: [ccp4bb] Looking for proteins for undergraduate biochemistry lab

2021-06-17 Thread Artem Evdokimov
s blue 2,6-dichloroindophenol into colorless reduced form that spontaneously reoxidizes back to blue in air And many others :) Artem On Wed, Jun 16, 2021, 6:19 PM P. H wrote: > Hello All, > > We are looking for some candidate proteins for an undergraduate level > advanced biochemist

Re: [ccp4bb] [OUT-OF-TOPIC] Compound service management CRO

2021-06-01 Thread Artem Evdokimov
Frontier Pretty good service, but definitely not the cheapest. Artem On Tue, Jun 1, 2021, 4:54 AM Wim Zhong wrote: > Hi Group, > > Does anyone have experience with CROs that can provide good compound > service management in terms of quality and cost? We are looking for a > pa

[ccp4bb] Research Associate position at SSRL-SMB

2021-05-28 Thread Artem Lyubimov
The Structural Molecular Biology (SMB) Division at the Stanford Synchrotron Radiation Lightsource (SSRL) is seeking a Research Associate with a strong background in X-ray diffraction data processing and/or software development. A successful candidate will work with an interdisciplinary group of cry

Re: [ccp4bb] crystallizing fusion proteins

2021-03-15 Thread Artem Evdokimov
omain that simply did not like the buffer conditions and was essentially insoluble after cleavage due to its bull properties' mismatch with those of the solvent. Artem On Mon, Mar 15, 2021, 5:08 AM Schreuder, Herman /DE < herman.schreu...@sanofi.com> wrote: > Dear Bulletin Board, &g

[ccp4bb] Off-topic: research associate job posting

2021-02-14 Thread Artem Evdokimov
4country%3DUnited+States&location_type=city&location_text=Boston%2C+MA%2C+United+States&location_autocomplete=true&radius=320 Artem Silicon Therapeutics (“SITX”) is a privately held, physics-driven integrated drug discovery company. SITX’s discovery efforts as well as physic

Re: [ccp4bb] OFFTOPIC question "Two plasmids in one host cell"

2021-01-03 Thread Artem Evdokimov
quantify it by dilution, transformation, and colony counting against a known standard plasmid. Happy new year Artem On Wed, Dec 30, 2020, 4:35 AM Anamika Singh wrote: > Hi All, > > I have two constructs having different ori, p15ori and M13 ori, different > promoters araBAD promoter a

Re: [ccp4bb] To solve the problem of an extremely asymmetric peak shape obtained from gel filtration chromatography

2020-12-09 Thread Artem Evdokimov
Probably a good idea to share an image :) worth many words... Artem On Wed, Dec 9, 2020, 9:17 AM wrote: > Dear All > There is a 43kd protein purified via Ni-chelating affinity > chromatography, anion exchange chromatography and gel filtration > chromatography in sequence.

Re: [ccp4bb] AW: [ccp4bb] External: Re: [ccp4bb] AlphaFold: more thinking and less pipetting (?)

2020-12-08 Thread Artem Evdokimov
t, I guess I am just saying that literature, IMO, has long ago stopped being generally directly reproducible. Not getting into the obvious reasons as to why it happened, but still sad that it happened. Artem On Tue, Dec 8, 2020, 8:28 AM Hughes, Jonathan < jon.hug...@bot3.bio.uni-giessen.de> wro

Re: [ccp4bb] Off-topic: Mild cross-linking protocol

2020-10-20 Thread Artem Evdokimov
free to write directly for/with additional details. Artem On Mon, Oct 19, 2020, 3:18 AM Chiara Bruckmann wrote: > Dear all, > > Sorry for the off-topic question. I need to prepare an heterodimeric > protein complex for an immunisation, and I would like to make sure that the > dimer

[ccp4bb] offtopic: three job postings @ Silicon Therapeutics

2020-10-05 Thread Artem Evdokimov
Dear CCP4 friends, I would like to let you know that we have just posted three jobs open within my team at Silicon Therapeutics. Qualified inquiries are welcome! Artem 1. Senior position in Biochemistry https://silicontx.com/careers/open-positions/senior-investigator-principal-investigator

[ccp4bb] slightly offtopic: antibody and nanobody development providers

2020-10-05 Thread Artem Evdokimov
would like to gather some new ones especially if people used them and liked the net result. Would be happy to summarize the outcome and distribute the summary in this list. Many thanks, Artem - Cosmic Cats approve of this message

Re: [ccp4bb] opinions about crystal soaking service providers

2020-09-21 Thread Artem Evdokimov
will post it here. Cheers, Artem - Cosmic Cats approve of this message On Fri, Sep 11, 2020 at 10:26 AM Artem Evdokimov wrote: > Dear CCP4ers! > > I would like to once again benefit from the communal wisdom and experience > of our community. Thank you in advance for your advice! >

[ccp4bb] opinions about crystal soaking service providers

2020-09-11 Thread Artem Evdokimov
(assuming there are enough replies to merit a summary). Many thanks! Artem - Cosmic Cats approve of this message To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUB

Re: [ccp4bb] ARP/WARP won't install - old glibc trouble

2020-09-04 Thread Artem Lyubimov
t;> Modified version exit status 1 >> >> -- after some digging I found several old, unsolved issues about that in >> GitHub, any ideas about how to get around? >> >> >> >> ------ >> >> To unsubscribe from t

Re: [ccp4bb] Advice on DNA negative staining

2020-08-04 Thread Artem Evdokimov
ntent/285/18/13349.full.pdf Artem - Cosmic Cats approve of this message On Tue, Aug 4, 2020 at 7:11 AM Panne, Daniel (Prof.) < daniel.pa...@leicester.ac.uk> wrote: > Hi Meytal, > > 1. The concentration seems way too high at 254mg/ml. Typically 0.1-5mg/ml > are used. >

Re: [ccp4bb] Protocol for bacmid transformation in E.coli

2020-07-18 Thread Artem Evdokimov
Yes It requires electroporation and very careful handling of the bacmid. Other than that it is a fairly simple process. Here is an example reference: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5067234/ Artem On Sat, Jul 18, 2020, 9:12 PM Digant Nayak wrote: > Dear all, > > Sorr

Re: [ccp4bb] Looking for suggestions with protein expression

2020-06-27 Thread Artem Evdokimov
with us the more we may be able to help you. Artem On Sat, Jun 27, 2020, 3:15 AM Umar Farook wrote: > Dear All, > > Sorry for an offtopic question, your suggestions are highly appreciated. > > We have been working on iron sulfur cluster binding protein, which is > usually expr

Re: [ccp4bb] Highest resolution of X-ray / neutron / electron crystallography, cryo EM

2020-06-09 Thread Artem Evdokimov
d their colleagues.” *Verb* “To discredit or invalidate an otherwise beautiful theory” Artem Artem - Cosmic Cats approve of this message On Tue, Jun 9, 2020 at 9:36 AM Tobias Beck wrote: > Dear all, > > I was asked by a student what the highest resolution is, for each of the > fo

Re: [ccp4bb] Question about small molecule crystallography

2020-06-01 Thread Artem Evdokimov
dot SHELX cup, it's one of my more treasured curios). Artem - Cosmic Cats approve of this message On Mon, Jun 1, 2020 at 6:01 PM Jiyuan Ke wrote: > Hi Everyone, > > I want to crystallize a small organic molecule. I have very limited > experience in small molecule crystallograph

Re: [ccp4bb] Fusion proteins to solubilize your protein

2020-05-05 Thread Artem Evdokimov
Artificial helix bundles GS SUMO Ubq NusA Fc and other mAb domains Nanobodies (as fusions) Cyt b562 Rubredoxin Flavodoxin VLR Barnase MHC proteins Bostjan Kobe wrote a paper in 2015 which you probably saw already. Artem On Tue, May 5, 2020, 2:45 PM Murpholino Peligro wrote: > I was wonder

Re: [ccp4bb] server to predict structural stability

2020-05-04 Thread Artem Evdokimov
Rosetta will do this. But it's not a server, and there is a fairly steep learning curve. Artem - Cosmic Cats approve of this message On Mon, May 4, 2020 at 6:04 AM Firdous Tarique wrote: > Hi > > I am trying to incorporate novel disulfide bond by introducing Cys > mutants

Re: [ccp4bb] somewhat off-topic :)

2020-04-28 Thread Artem Evdokimov
Thank you Artem On Tue, Apr 28, 2020, 7:22 PM Thomas Cleveland wrote: > Hi, > > There are tons of these listed on eBay, many in very good condition or > even unused. I used to get them there all the time. > > Best > > On Tue, Apr 28, 2020 at 8:51 AM Artem Evdokimov &g

Re: [ccp4bb] somewhat off-topic :)

2020-04-28 Thread Artem Evdokimov
Thank you very much! Artem On Tue, Apr 28, 2020, 1:03 PM Guenter Fritz < guenter.fritz.phenix.c...@gmail.com> wrote: > Dear Artem, > > I am a fan of the former "Superformance" column from Merck. The production > / selling of these columns is sourced out to a small

[ccp4bb] somewhat off-topic :)

2020-04-28 Thread Artem Evdokimov
deal. I was already looking at Bio-Rad and found them almost as expensive, so I am actually looking for some sort of 'knockoff' manufacturer :) Thank you Artem - Cosmic Cats approve of this message To unsubscribe f

Re: [ccp4bb] insect secretion recommendations?

2020-04-20 Thread Artem Evdokimov
Gentle spin followed by TFF - a cheap peristaltic pump plus $200 filter cartridge will do the trick. Artem On Mon, Apr 20, 2020, 11:56 AM Gloria Borgstahl wrote: > Hi Friends, We are secreting Spike Ecto domain into the media from insect > cells for purification. As we scale u

Re: [ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] on-topic: your opinions requested!

2020-04-07 Thread Artem Evdokimov
cases like this, I normally choose not to publish, but maybe their bosses insisted. Anyway, many options to find excuses, but it looks like Artem has to go solve this structure himself. Thank you all very much, many good responses :) Arte, - Cosmic Cats approve of this message On Tue, Apr 7, 202

[ccp4bb] on-topic: your opinions requested!

2020-04-07 Thread Artem Evdokimov
u're working on this, which is not necessarily great since you're competing), or to just buck up and do the structure on your own (which feels a bit wasteful). Then, you realize that your friends at CCP4 have a lot of wisdom to offer, so you sit down and pen an

[ccp4bb] off-topic: coronavirus test summaries

2020-04-04 Thread Artem Evdokimov
> https://www.finddx.org/covid-19/pipeline/ May be this saves someone twenty minutes of searching online. Artem - Cosmic Cats approve of this message To unsubscribe from the CCP4BB list, click the following link: https://www.jis

Re: [ccp4bb] SARS-CoV-2 test on a smartphone

2020-04-02 Thread Artem Evdokimov
equipment that may be available in good (sadly, not all) high school labs. Artem On Thu, Apr 2, 2020, 3:17 PM Jurgen Bosch wrote: > Hi Artem, > > How would you do this in resource limited countries? > I think James idea is pointing toward that direction, deliver an easy to > appl

Re: [ccp4bb] SARS-CoV-2 test on a smartphone

2020-04-02 Thread Artem Evdokimov
human IgG and IgM antibodies, label them a bit and do Homebrew ELISA on serum. Artem Artem On Thu, Apr 2, 2020, 11:28 AM James Holton wrote: > Personally, if I were infected with SARS-CoV-1 instead of SARS-CoV-2 I'd > still like to know that. > > It is most certainly true that

[ccp4bb] off-topic: work opportunities at Enko

2020-03-30 Thread Artem Evdokimov
n more, informally - please feel free to write me directly (2) if you'd like to apply, please write to *care...@enkochem.com* Artem VP of Biochemistry/Molecular Biology Enko To unsubscribe from the CCP4BB list,

Re: [ccp4bb] Expi 293 (Met-) expression medium for selenomethionine labeling

2020-03-15 Thread Artem Evdokimov
they did, this is a nice product and it ought to be a good money-maker for them) Artem - Cosmic Cats approve of this message On Sun, Mar 15, 2020 at 5:27 PM Lau Kelvin wrote: > Dear Artem, > > > By work poorly do you mean, not as well and are you referring to all Expi > cells? >

Re: [ccp4bb] Expi 293 (Met-) expression medium for selenomethionine labeling

2020-03-11 Thread Artem Evdokimov
ability to use the L-SeMet pure as opposed to the more common L,D-mix then you can put in more. Either way, it works. Expect your yield to suffer. Question: did you try iodine incorporation? You can do it on the level of pure protein, or crystals... Artem - Cosmic Cats approve of this message

Re: [ccp4bb] Mixed oligomeric states in crystallo

2020-02-02 Thread Artem Evdokimov
short helix. Nature is cruel, but interesting. Artem On Fri, Jan 31, 2020, 10:33 AM Kluenemann, Thomas < thomas.kluenem...@helmholtz-hzi.de> wrote: > Dear all, > > > > We recently solved a the structure of a small c-type cytochrome. We > observed, that of the eleven chain

Re: [ccp4bb] AW: [ccp4bb] Urea vs. Guanidinium/HCl

2020-02-02 Thread Artem Evdokimov
then to crash the aggregate out. This is of course somewhat extreme and cannot be recommended as a general solution to every issue of this sort. Addition of the right detergent can also help. Separation via another orthogonal matrix is often helpful as well. Artem On Sun, Feb 2, 2020, 4:22 AM

Re: [ccp4bb] Urea vs. Guanidinium/HCl

2020-02-01 Thread Artem Evdokimov
. Artem On Sat, Feb 1, 2020, 6:22 PM Jon Hughes wrote: > Hello everyone, > We work on a protein that tends to aggregate. The process is slowed but not > stopped by glycerol and NDSB201. Interestingly, whereas guanidinium/HCl > dissolves the aggregate readily, urea just turns it into

Re: [ccp4bb] microscope camera

2019-11-27 Thread Artem Evdokimov
I bought a bunch of cheap cameras from Amscope. They were OK for the price. Artem On Wed, Nov 27, 2019, 12:46 Dean Derbyshire wrote: > Forgive the off topic subject: > > > > Has anyone got any experience with moticam microscope cameras? > > We are looking into cheap camer

Re: [ccp4bb] Fwd: [ccp4bb] suggestions on small proteins that for a complex

2019-11-10 Thread Artem Evdokimov
FliS and FliC Artem On Sun, Nov 10, 2019, 03:42 Gianluca Cioci wrote: > ps: the 3D structure > of the complex should > be solved at high resolution > > ;o) > > > > > Dear All, > > I am looking for examples of two small proteins A and B that can form

[ccp4bb] Off topic: 384 well stamper

2019-11-08 Thread Artem Evdokimov
machinery (any personal impressions of these and any other similar LH devices are very welcome!). I would be happy to post a condensed summary of replies. Thank you Artem To unsubscribe from the CCP4BB list, click the following

Re: [ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] Occupancy refinement of overlapping electron density of a residue and ligand

2019-11-07 Thread Artem Evdokimov
I am willing to bet that the ketone is covalently reacting with the arginine and the result is what you see :) Artem - Cosmic Cats approve of this message On Thu, Nov 7, 2019 at 3:33 AM wrote: > Dear HK, > > In your case mass spec would be extremely valuable. Not only could it &

Re: [ccp4bb] lysine methylation in E. coli?

2019-11-05 Thread Artem Evdokimov
It happens. Ef-Tu is methylated on a single lysine Also LafV is a putative methylase in E. Coli but its effects were not studied in detail. Salmonella methylates flagellin which is how lysine methylation was discovered - and E.coli is a kissing cousin so... Artem On Tue, Nov 5, 2019, 12:31

Re: [ccp4bb] Sodium Ion Binding?

2019-11-03 Thread Artem Evdokimov
other methods) Overall the key component to these methods is your ability to displace the sodium with something else prior to measuring the effect of titration the ion back. Isotopic Na is easier in this regard - but at a cost... Hope this helps. Artem https://bmcresnotes.biomedcentral.com/articles

Re: [ccp4bb] off topic: microscope in glove box

2019-10-21 Thread Artem Evdokimov
d together in a single tube with air trapped between them - if the 'vent' is blocked (by e.g. old grease or something) then these may pop. https://www.olympus-lifescience.com/en/microscope-resource/primer/anatomy/oculars/ But the short version is right 99% of the time. Artem *"Pr

Re: [ccp4bb] challenges in structural biology

2019-07-24 Thread Artem Evdokimov
Unlimited length in an hour is physically unlikely, but the rest is not that far off I think. We are at or below 1 cent per basepair already (in bulk)... Artem On Wed, Jul 24, 2019, 13:01 Keller, Jacob wrote: > Yes, imagine 1 hr, tabletop, unlimited-length, error-free, dirt-cheap g

[ccp4bb] off topic: job posting

2019-07-22 Thread Artem Evdokimov
Good morning, We have two relevant job postingings that I would like to share. Thank you for your attention :) Artem https://careers.massbio.org/job/sr-scientistprincipal-scientist-computational-chemistry/49455467/ and https://careers.massbio.org/job/scientist-enzymology-protein-chemistry

Re: [ccp4bb] challenges in structural biology

2019-07-21 Thread Artem Evdokimov
s a bit of a distraction from James' original point. However it's a valid opportunity for a lively discussion on its own :) Artem - Cosmic Cats approve of this message On Sun, Jul 21, 2019 at 4:52 PM Kay Diederichs < kay.diederi...@uni-konstanz.de> wrote: > Dear Artem

Re: [ccp4bb] challenges in structural biology

2019-07-21 Thread Artem Evdokimov
oblem #1 with this attitude (and an equivalent of a very large army's worth in funding) then it can be solved. Artem - Cosmic Cats approve of this message On Sun, Jul 21, 2019 at 1:55 PM Kay Diederichs < kay.diederi...@uni-konstanz.de> wrote: > Hi Artem, > > you are certain

Re: [ccp4bb] challenges in structural biology

2019-07-21 Thread Artem Evdokimov
predictable and artful phenomenon while literally all other aspects of structure determination process (the gene to structure pipeline, whatever you might call it)have made astronomic leaps forward. Artem - Cosmic Cats approve of this message On Mon, Jul 15, 2019 at 3:44 PM Holton, James M <

[ccp4bb] multiple openings at Enko

2019-05-01 Thread Artem Evdokimov
ob/plant-biology-research-assistant/48155606/> - Patent Liaison <https://careers.massbio.org/job/patent-liaison/48155601/> (all the links above are from MassBio website and can be separately located by searching for 'Enko') Please direct inquiries/submissions to care...@en

Re: [ccp4bb] Interesting pattern on a crystallization drop

2019-03-27 Thread Artem Evdokimov
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

Re: [ccp4bb] KCl in SDS-PAGE workarounds?

2019-03-03 Thread Artem Evdokimov
. Precipitation of protein prior to the gel is certainly an option, although some proteins have difficultues with recovering after that (membrane proteins in particular). Artem - Cosmic Cats approve of this message On Sat, Mar 2, 2019 at 9:53 PM Keller, Jacob wrote: > Dear crystallographers, > > &

Re: [ccp4bb] ionic strength for extraction buffer of membrane proteins

2019-03-02 Thread Artem Evdokimov
high salt, and often would do better in sodium acetate as opposed to chloride. I've worked with ion channels that preferred 3M NaCl, or 2M MgCl2 and other fairly weird conditions... Artem - Cosmic Cats approve of this message On Fri, Mar 1, 2019 at 7:27 AM Alex Perálvarez Marín wrote: >

Re: [ccp4bb] Fwd: dry Shipper made in China

2019-01-26 Thread Artem Evdokimov
Dry shippers are often featured on auction sites for used equipment and sometimes can be found for huge discounts... Artem - Cosmic Cats approve of this message On Fri, Jan 25, 2019 at 8:36 AM Muhammad Imran wrote: > Dear Community members, > > We wanted to buy molecular dime

Re: [ccp4bb] looking for 10-20 kDa proteins that express well and migrate appropriately on SDS-PAGE

2019-01-06 Thread Artem Evdokimov
) Ferredoxin Rubredoxin cytochrome b562 Ubiquitin the list goes on and on... As to polycistronic stuff - it may be easier to mix lysates than to mess around with multiple expression cassettes - in case you'd want to change the mix later... just my two cents. Artem - Cosmic Cats approve of

Re: [ccp4bb] Non-Cysteine modification with heavy atom

2019-01-02 Thread Artem Evdokimov
ronment I am probably missing another 10-15 methods but gotta run :) Artem - Cosmic Cats approve of this message On Wed, Jan 2, 2019 at 2:42 PM Chandramohan Kattamuri < 1c5b7cb6c764-dmarc-requ...@jiscmail.ac.uk> wrote: > > Dear CCP4 members, Can someone suggest to me a met

Re: [ccp4bb] 2019 New Year’s resolutions of a cryo-EM newbie

2019-01-02 Thread Artem Evdokimov
My apologies for posting this on an open board :) I realize that this is completely off topic - but it is a pretty painful topic that affects us all regardless of academic or industrial affiliation, professional preferences etc. Artem --- do not read below unless you want to :) --- If an

Re: [ccp4bb] 2019 New Year’s resolutions of a cryo-EM newbie

2019-01-01 Thread Artem Evdokimov
https://www.unboundworlds.com/wp-content/uploads/2016/05/takei-oh-my.jpg oh, my... Happy new year! Artem - Cosmic Cats approve of this message On Tue, Jan 1, 2019 at 5:38 PM Marin van Heel < 057a89ab08a1-dmarc-requ...@jiscmail.ac.uk> wrote: > 1) I shall not make false FSC r

Re: [ccp4bb] opentrons pipetting robot

2019-01-01 Thread Artem Evdokimov
is sort of like a large 3D printer chassis with a deck and pipettors bolted on. If you love to tinker this is a machine for you. Cannot beat the price. Artem On Mon, Dec 31, 2018, 12:46 Doug Juers Hello All, > > I've just learned about the opentrons pipetting robot, which appears to

Re: [ccp4bb] Adding Zinc to Protein

2018-12-30 Thread Artem Evdokimov
t EDTA, its complex with Zn is far too stable) and then add it directly to your protein - note that adding Zn to protein directly tends to cause precipitation (but chelating the Zn with a moderate-strength agent tends to prevent this). Good luck, Artem - Cosmic Cats approve of this message On Su

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