[ccp4bb] AW: [ccp4bb] off-topic:fluorescence polarization displacement assay

Dear Megha, I am puzzled by the results you presented. If you only see the effect in the presence of your protein, the protein must have something to do with it. The steep decline points to some highly cooperative effect, which might be aggregation/precipitation. Did you check that your

Re: [ccp4bb] off-topic:fluorescence polarization displacement assay

Hi Megha, my explanation would be that you have a 2:2 complex. Meaning in your standard assay, you need 2 peptides as dimer to get a dimer of your protein. Now that you do the competition assay, you probably start with concentrations, where this 2:2 complex is not saturated yet. Meaning

Re: [ccp4bb] Se-Met and Se-Cys double labelling

We have successfully used non-auxotrophic strains for incorporation of SeMet and SeCys, with an incorporation level of >80% and no effects on yield or solubility. Details can be found here: http://scripts.iucr.org/cgi-bin/paper?S0907444910042022 It's a straight-forward protocol and structure

Re: [ccp4bb] Questions about antibody in crystallization

The fact that the PDB holds hundreds of FABs and a handful whole ABs suggests to me that the latter are hard to get crystals for. So, all the more reason for us bioinformaticians that you, experimentalists try it :-) Gert On 22-6-2017 20:39, Cheng Zhang wrote: Hi all, I have a naive

[ccp4bb] AIMLESS unmerged MTZ output

Hello all, Are the following statements regarding AIMLESS unmerged mtz output accurate? - the H, K, L, M/ISYM columns are sufficient to recover the "original" H K L indices. - a combination of "original" H K L and the BATCH value is unique inside the file. Thank you in advance. Wolfram Tempel

[ccp4bb] Questions about antibody in crystallization

Hi all, I have a naive question about antibodies. Many people used Fab fragments in crystallization. I am wondering if it is possible to use the whole IgG molecule with Fc fragment as well. Or it would be too flexible and bad for crystallization? Thanks, Cheng -- - Cheng

Re: [ccp4bb] Se-Met and Se-Cys double labelling

Dear Vito AMPLE is another option to easily and automatically find conserved cores among a set of distant homologues. You point it to a directory containing your homologues and use the -homologs True flag. You can use the command line or CCP4i. It will then use GESAMT to find the multiple

Re: [ccp4bb] Questions about antibody in crystallization

Yes, the hinge region between Fab and Fc is highly flexible. If you look at IgG by EM you will see many different conformations. Best to use Fab or scFv. Jarrod Mousa On Thu, Jun 22, 2017 at 1:39 PM, Cheng Zhang wrote: > Hi all, > > I have a naive question about

Re: [ccp4bb] Se-Met and Se-Cys double labelling

I have only heard of a few cases of successful Se incorporation into Cys, and none of them sounded like fun. Sounds like you have gotten a few suggestions already. There is not much literature on this. As for alternative solutions to your original question, I can tell you the success or

[ccp4bb] Course: Bridging solution methods: from NMR to X-ray scattering and biophysics"

Dear all, Announcing in the mailing list for crystallography and in the era of the single particles EM resolution revolution, a course for solution methods? NMR, SAXS, calorimetry, fluorescent methods and modeling? Seriously? Well, yes! For many, many reasons, you should be at least curious,

Re: [ccp4bb] What are acceptable Rwork/Rfree for publication

Dear Gerard, I was puzzled by the statement that the UCLA anisotropy server characterises anisotropy in terms of a combination of effects restricted to lie along the crystallographic axes. That server is built on the anisotropy correction algorithm in Phaser, and from the beginning Phaser has

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A postdoctoral or technician position is immediately available in the Structural Biology of Noncoding RNAs and Ribonucleoproteins Section, Laboratory of Molecular Biology (LMB), NIDDK, in NIH’s vibrant main campus in Bethesda, MD near Washington DC. The lab addresses a widening gap between the

Re: [ccp4bb] AIMLESS unmerged MTZ output

I believe so! Eleanor On 22 June 2017 at 17:04, wtempel wrote: > Hello all, > > Are the following statements regarding AIMLESS unmerged mtz output > accurate? > - the H, K, L, M/ISYM columns are sufficient to recover the "original" H K > L indices. > - a combination of

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A postdoctoral position is available immediately in the laboratory of Dr. Emilia Galperin in the Department of Molecular and Cellular Biochemistry in the College of Medicine at the University of Kentucky to work on externally funded, multi-year projects. The overall goal of the lab is to

Re: [ccp4bb] AIMLESS unmerged MTZ output

Yes. With the caveat that ISYM refers to the symmetry operators in the order they are stored in the MTZ file Phil Sent from my iPhone > On 22 Jun 2017, at 17:04, wtempel wrote: > > Hello all, > > Are the following statements regarding AIMLESS unmerged mtz output accurate?

Re: [ccp4bb] Se-Met and Se-Cys double labelling

Yes, I agree that MR is worth a shot, though depending on the resolution your life may be vastly easier with experimental phases! We've had several cases where the following kind of procedure works: find related structures with a very sensitive homology search (we like HHPRED, though other