Re: [ccp4bb] salt bridges etc..

Thank you Gert - very clear explanation.. Eleanor On 16 July 2018 at 13:31, Gert Vriend wrote: > Dear Eleanor, > > Salt bridges are a compromise between entropy and enthalpy. If, say, an > Asp and an Arg side chain are a bit restricted in their freedom and the > charges are close, enthalpy

Re: [ccp4bb] salt bridges etc..

Dear Eleanor, Salt bridges are a compromise between entropy and enthalpy. If, say, an Asp and an Arg side chain are a bit restricted in their freedom and the charges are close, enthalpy wins, and if they are very exposed, and not close at all, entropy wins. The enthalpic gain upon protein

[ccp4bb] salt bridges etc..

How do people decide on what is a salt bridge within a molecule and how to count them for those Tables? I have been looking at 2z2f - paper claims some score..- But there are several residues in alternate conformation with NZ A to OE1Aand NZ A to OE1B and NZ B to OE1B etc Is that one

Re: [ccp4bb] Salt or protein?

Thanks your suggestions! I tried Dials but couldn’t get any further. There just too few spots like Artem suggested. I’ll follow Patrick’s advice to seed a new screening with this crystal. This one was really tiny. I may get a bigger one. Jan > On Feb 17, 2018, at 2:43 PM, Harry Powell

Re: [ccp4bb] Salt or protein?

Hi Jan What happens if you use a program that can easily use spots from all images to index, like DIALS or XDS? My recollection (which may be wrong) is that this is not straigthforward in HKL3000. > On 17 Feb 2018, at 19:32, Jan van Agthoven wrote: > > Dear all, > At

[ccp4bb] AW: [ccp4bb] Salt bridge-hydrogen bonds

@JISCMAIL.AC.UK] Im Auftrag von Mohamed Noor Gesendet: Freitag, 20. Januar 2017 11:45 An: CCP4BB@JISCMAIL.AC.UK Betreff: [ccp4bb] Salt bridge-hydrogen bonds Dear all Is it possible for two residues to form a salt bridge between them, and at the same time**, each of them form a hydrogen bond

[ccp4bb] Salt bridge-hydrogen bonds

Dear all Is it possible for two residues to form a salt bridge between them, and at the same time**, each of them form a hydrogen bond with another residue? In other words: Arg1 - Glu10 (salt bridge) Arg1 - Tyr600 (H bond) Glu10 - Thr590 (H bond) ** I understand proteins are not static

[ccp4bb] Salt!

I have been attempting to obtain a protein crystal of my protein for just over 2 years at this point. We have attempted removing the tag, binding the protein to its ligand, removing as much salt as possible (crashes at at too low a salt concentration)--this lead us to try reverse vapor

Re: [ccp4bb] Salt!

Hi Catherine, If they are indeed salt crystals, have you tried preparing different truncations of the gene encoding your target? I've seen a number of successes in which, after a codon or two was added to the termini of the gene being overexpressed, the target crystallized beautifully. Best,

Re: [ccp4bb] Salt!

Hi Catherine, What buffer salt do you have your protein in when you set up screens - maybe this is leading to your salt crystal issues? How long does it take for the salt crystals to appear? Have you tried setting up trays at different temperatures? Microbatch crystallisation under oil?

Re: [ccp4bb] Salt!

Hi Catherine, first of all, I'm sorry that you're feeling so frustrated. In addition to the many sensible suggestions that you're surely going to read here, I would like to point you to a paper I read a while ago in Nature: In situ proteolysis for protein crystallization and structure

Re: [ccp4bb] Salt!

...@hwi.buffalo.edu Telepathy: 42.2 GHz Heisenberg was probably here! From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Bishop, Catherine E. Sent: Wednesday, July 16, 2014 10:56 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Salt! I have been attempting to obtain a protein crystal of my

Re: [ccp4bb] salt or not?

Careina, One thing to try if other ideas don't work or are too difficult, is covalently (therefore unambiguously) labelling a little of your protein with a fluorescent dye. If you add 20 nL of this to the drop *after the crystals have grown*, protein crystals will light up, but salt crystals

[ccp4bb] salt or not?

Dear ccp4 I have been performing trials on a protein DNA complex for a while now and have not seen any crystals form. Today I checked an old plate (over a month old) and I see 4 large crystals. *excitement* Three of them look tetragonal in shape (like a pyramid) and one of them looks

Re: [ccp4bb] salt or not?

@astrazeneca.com mailto:name.surn...@astrazeneca.com Please consider the environment before printing this e-mail From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Careina Edgooms Sent: 15 April 2013 11:18 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] salt or not? Dear ccp4 I have

Re: [ccp4bb] salt or not?

From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] On Behalf Of Careina Edgooms [careinaedgo...@yahoo.com] Sent: 15 April 2013 11:18 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] salt or not? Dear ccp4 I have been performing trials on a protein DNA complex for a while now and have not seen any

Re: [ccp4bb] salt or not?

Dear Careina, altough your crystals does't take up the Izit dye it sounds promising. The uptake of Izit depends on the solvent channels of the protein molecule - sometimes the dye just can't enter the molecule. Concerning the Calciumchloride - if the concentration is not too high and without

Re: [ccp4bb] salt or not?

I may be biased, but the only way to really be sure is to shoot them. If you see no spots at all, be sure to do a wide oscillation (rotation during the exposure) shot as well. It is not unlikely for a salt crystal to be oriented so that no relps are on the Ewald sphere, giving no spots.

Re: [ccp4bb] salt or not?

Protein-DNA complex crystal with channels too small for the dye is *extremely* unlikely, imho. Original message From: Ulrike Demmer ulrike.dem...@biophys.mpg.de Date: 04/15/2013 8:48 AM (GMT-05:00) To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] salt or not? Dear

Re: [ccp4bb] Salt bridge in crystallization

In think most of the salt bridges I recall in structures are either in the core of the protein or in interfaces (crystallin or complex interfaces with little or no polar solvent around). Just like charge interactions, the lower dielectric constant of the environment makes them stronger.

[ccp4bb] Salt bridge in crystallization

Dear All, A lot of 3-D crystal structures highlight the salt bridges in the structure, although some structures of them are got at high salt concentrations. Will you please explain to me why the protein salt bridge can still exist in the high salt concentration as used in the crystallization

Re: [ccp4bb] Salt bridge in crystallization

On 10/19/2012 10:37 PM, Acoot Brett wrote: Will you please explain to me why the protein salt bridge can still exist in the high salt concentration as used in the crystallization condition? You are saying it as if there is some fundamental law of nature that says that salt bridges cannot

Re: [ccp4bb] salt or protein...

Sorry Jay, They are for sure phosphate crystals. They always looked like that. psp On Sun, May 29, 2011 at 5:18 PM, Jayashankar s.jayashan...@gmail.com wrote: Dear Friends , I need to know whether phosphate can form hexagon shaped crystals. In one particular condition i have 4 different

[ccp4bb] salt or protein

Dear Jayashankar, I had several instances where salt crystals of the same component takes different morphologies. So it is very possible, as it appears that the hexagonal forms are also those of the salt components in the precipitant/buffer. You can confirm the

Re: [ccp4bb] salt or protein crystals?

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] salt or protein crystals?

Definitely small molecule crystals. You might want to push the detector closer and use better cryo solution for further confirmation. Nian On Tue, Dec 7, 2010 at 8:14 AM, xiuwen zhang congru...@gmail.com wrote: Dear Colleagues,     Currently we got several very tiny crystals. After exposuring

Re: [ccp4bb] FW: [ccp4bb] salt sensitive complex

Dear All: I am sorry that I did not know the policy. And thanks a lot for the kind reminder. Jerry CC: CCP4BB@JISCMAIL.AC.UK From: [EMAIL PROTECTED] Subject: Re: [ccp4bb] FW: [ccp4bb] salt sensitive complex Date: Thu, 31 Jan 2008 09:37:01 +0100 To: [EMAIL PROTECTED] Dear all

Re: [ccp4bb] salt sensitive complex

Dear All: Firstly I would like to thank many folks here for giving me great ideas several days ago. The following are some updates for this question. I did ITC experiments again using 25mMTris(pH8), 60mM NaCl(low salt condition). But things still turn out to be a

Re: [ccp4bb] salt sensitive complex

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,

[ccp4bb] salt sensitive complex

Dear All: Recently I am pursuing the crystallziation of a complex formd by two individual proteins and I met several interesting problems though they are kind of off-topic. Any suggestions for these problems will be highly appreciated. BIAcore showed about

Re: [ccp4bb] salt or protein?

Multiple overlapping salt lattices can sometimes look like protein diffraction, as long as you're looking in only two dimensions. However, if you can find the dominant rings, you should be able to discriminate since the c-spacing of salt would nearly always be pretty small. Consider powder

Re: [ccp4bb] salt or protein?

Hi Sreeram, assuming you have plenty of those crystals, why don't you loop a few pass them through a drop of your reservoir for washing and load them on a SDS gel ? Juergen Sreeram Mahesh wrote: Hi All! I have been trying to screen for my protein crystals, from the crystals grown