Re: [ccp4bb] Cysteine-S-Iodine interaction

I’m late to the party here, but there are (at least) 59 instances of a C-S-I fragment in the CCDC. Flipping through the first third of the list, GIGBED (triphenylmethyl-iodo-sulfane) seems somewhat close. The S-I bond is 2.41Å and the C-S-I bond angle is 105.4 degrees. There may be better ones

Re: [ccp4bb] TWIN?

It’s difficult to tell exactly what is happening from your description and the attached image. Both your description and the image are OK. It’s just that there are a lot of ways for things to go off the rails. Are the molecules stacked end-to-end? In that case, you may have an incommensurate

Re: [ccp4bb] Covalent Cysteine Aduct

My guess would be that the chains were prepared under reducing conditions, mixed, and then allowed to oxidize. The surface adduct could easily form during this process. On Mar 27, 2020, at 4:38 PM, Cowan, Richard H. (Dr.) mailto:rc...@leicester.ac.uk>> wrote: Hi, The Fab constructs have a

Re: [ccp4bb] Ligand identification

My only comment is that you should consider not only what is in reservoir, but also anything present in your sample buffer. On Jul 18, 2019, at 3:02 PM, Nicola Evans <251ca3b4615e-dmarc-requ...@jiscmail.ac.uk> wrote: (well conditions:

Re: [ccp4bb] beryllium chloride

Bob, Yes, Be salts are wildly toxic. They are also useful in structural studies on enzymes that perform phosphoryl transfers, almost always as beryllium fluoride complexes. The PDB contains about 200 such structures. Craig On Apr 1, 2019, at 9:37 PM, Sweet, Robert

Re: [ccp4bb] beryllium chloride

You can purchase beryllium oxide through a number of vendors. After careful neutralization with an appropriate amount of HCl, you should have BeCl2 in solution. I usually use pH paper to check the pH in such small volume operations. > On Apr 1, 2019, at 4:07 PM, Alexandra Deaconescu > wrote:

Re: [ccp4bb] RNA pdb molecular weight

I’m guessing you need to be closer than ~320 atomic mass units per ribonucleobase? (Which neglects modified bases and counter ions and assumes 25% each of ACGU?) On Nov 16, 2018, at 10:19 AM, Reza Khayat mailto:rkha...@ccny.cuny.edu>> wrote: Hi, I’m not an RNA person. Can anyone suggest a

Re: [ccp4bb] To post to ccp4bb...

A phospholipid headgroup might be rotationally disordered and washed out, especially if it isn’t exactly the correct binding partner. It does look very much like lipid density to me. Attempts to model a diacyl glycerol and PEGs should be revealing. On Jul 2, 2018, at 10:36 AM, Edward A. Berry

Re: [ccp4bb] help identifying unknown density

You may have crystallized an enzyme that uses a phosphoramidate intermediate. https://en.wikipedia.org/wiki/Phosphoramidate On Oct 9, 2017, at 10:40 AM, Stephen Cusack > wrote: Dear All, I am refining the crystal structure of an E. coli expressed

Re: [ccp4bb] A question about Cys and fluoro benzene ring

As others have suggested, it looks very much like a substitution at the fluorine position. I might add that high resolution electrospray mass spec should be very useful in this case, because I suspect that this adduct will survive sample preparation, and it would provide strong and orthogonal

Re: [ccp4bb] Unknown positive electron density

h is smaller than the coordination distance between Ba and water, we are skeptical of the Ba being there. https://cbsostorage.chem.umd.edu/owncloud/index.php/s/O4lI2iKvRsQUoRo Thank you, Betty On Mon, Aug 21, 2017 at 5:21 PM, CRAIG A BINGMAN <cabing...@wisc.edu<mailto:cabing...@wisc

Re: [ccp4bb] Unknown positive electron density

What is the data collection wavelength/energy? Would you expect significant anomalous diffraction from As at this wavelength? On Aug 21, 2017, at 11:37 AM, Betty Chu > wrote: Hi Shailesh, When I modelled in the Barium ion with octahedrally coordinated

Re: [ccp4bb] large number in ASU

Congratulations! I think you are now looking for additional crystallographic and non-crystallographic symmetry, because finding 40 particles in arbitrary positions and orientations is going to be brutal. I wouldn’t take the cell and point group assignment from XDS at face value. Rather I

Re: [ccp4bb] [ccp4bb] protein precipitation reg

Since I’m in full-on cranky old biochemist mode now, I think that vitriol is an old name for sulfuric acid. > On Mar 29, 2017, at 8:40 PM, Keller, Jacob wrote: > >> And if we are going to pour scorn and vitriol on Tris, why not mention its >> large dpKa/dT of 0.03 pH

Re: [ccp4bb] [ccp4bb] protein precipitation reg

> On Mar 29, 2017, at 4:15 PM, Chun Luo wrote: > > In addition to price, the prevalence of Ni purification may be another reason > for Tris popularity. Some His-tagged constructs don't bind to Ni well in > HEPES. I wonder if anyone has similar experience or comments. —Chun

Re: [ccp4bb] [ccp4bb] protein precipitation reg

There are almost always better choices than Tris buffer. Mo Cleland used to call it “Trash” buffer. He is no longer with us, but today I will happily carry that flag in his honor. Tris may show up in your crystal structure, especially at carbohydrate binding sites. Tris may be a surprisingly

Re: [ccp4bb] No improvement in R-factor after Refmac.

You really need to approach such situations with caution. Examination of the relatively small number of axial reflections probably show that there might be twofold screw axes in all three directions. But a non-crystallographic microscopic translation of nearly 0.5 in the direction of a

Re: [ccp4bb] Crystallization with no precipitant

On Mar 1, 2017, at 8:19 PM, Shaun Lott > wrote: They diffracted, but weren't much use to us in the end, as they were hard to reproduce or optimise. Hopefully you have more luck than we did! This sometimes happens with extremely soluble

Re: [ccp4bb] Crystallization with no precipitant

> Could it be possible that the robot never dispensed the reservoir solution > and the protein just crystallized against the reservoir solution through > simple concentration? I have just set up a couple of drops just against > reservoir solution. If this is the case, has anyone else

Re: [ccp4bb] Crystalization in low PH

I'm not convinced that you need a conventional buffer at pH 2 or 3. At pH 2, the hydrogen ion concentration is 10 mM. If you want to use something else, the second pKa for sulfuric acid is around 2. The first pKa for phosphoric acid is slightly higher than 2. Lactic acid has a pKa close to

Re: [ccp4bb] yellow crystals

In another thread, you indicated that there were no identifiable cofactor binding sites in your protein, so we are down to less common situations. Some proteins are spontaneously decorated with pyridoxal on surface lysine residues. In some cases, this has absolutely nothing to do with the

Re: [ccp4bb] atomic scattering factors in REFMAC

That is correct. We saw this in every selenomethionyl protein structure that was determined at CESG. There are two reasons for the negative density defects at Se atoms. As you note, the default scattering factors for Se are incorrect for these experiments, as f' is large in Se SAD

Re: [ccp4bb] raw data deposition

I strongly suspect that it is much more cost effective to have the PDB archive a unit of data than it is to have it archived at the lab or department level. So I suspect that more money will be available for doing science if we turn over archival responsibilities for image data to the kind

Re: [ccp4bb] IUCr committees, depositing images

On Oct 16, 2011, at 4:18 PM, Bosch, Juergen wrote: The rest is comparable to a collection of stamps, although with the benefit as BR mentioned of adding an additional hurdle/layer to falsifying structures. Not if you are interested in scattering that falls between reciprocal lattice maxima,

Re: [ccp4bb] IUCr committees, depositing images

I'm simultaneously embarrassed to have not read the thread to completion before replying, and also totally pumped that I would answer a question the same way as Bernhard Rupp! On Oct 16, 2011, at 7:34 PM, Bernhard Rupp (Hofkristallrat a.D.) wrote: Ø Not if you are interested in scattering

Re: [ccp4bb] should the final model be refined against full datset

Recent experience indicates that the PDB is checking these statistics very closely for new depositions. The checks made by the PDB are intended to prevent accidents and oversights made by honest people from creeping into the database. Getting away with something seems to imply some intention

Re: [ccp4bb] should the final model be refined against full datset

We have obligations that extend beyond simply presenting a best model. In an ideal world, the PDB would accept two coordinate sets and two sets of statistics, one for the last step where the cross-validation set was valid, and a final model refined against all the data. Until there is a

Re: [ccp4bb] is codon optimization worth it?

Rosetta strains carry a plasmid that supplies several tRNAs that match codons that are rare in E. coli. This is quite different than being explicitly optimized to express mammalian proteins. We (the Center for Eukaryotic Structural Genomics, a PSI-1 and PSI-2 center) used strains with the

Re: [ccp4bb] Database of Known Medically-Relevant Mutations

I agree with Ethan that this is a niche that OMIM fills with some (considerable) degree of success. http://www.omim.org/ Uniprot is also covering this in more detail, both in individual protein records, and in aggregate, e.g. http://www.uniprot.org/docs/humpvar On Sep 27, 2011, at 1:52 PM,

Re: [ccp4bb] Aging PEGs

Commercial polyethylene glycol is contaminated with polymers that have aldehyde groups at the ends. Other impurities include some amount of internal epoxide linkages. The aldehyde groups can be additionally oxidized to carboxylic acids. I would assume that oxidation to terminal carboxylic

Re: [ccp4bb] anomalous scatterer

This is from Ethan's very useful site, which should be known to everyone doing protein work at synchrotron sources:http://skuld.bmsc.washington.edu/scatter/http://skuld.bmsc.washington.edu/scatter/AS_form.htmlThe usual caveats apply... these calculations, especially for f", are often not