[ccp4bb] 2nd Australian Advanced Methods in Crystallography Workshop - New registration deadline

Dear all, The registration deadline to the 2nd Australian Advanced Methods in Crystallography Workshop has been extended. Registration deadline: 6th May 2014 Workshop dates: 22-25th June 2014 Website: https://events.synchrotron.org.au Contact: xtalworkshop2..

[ccp4bb] Problem with making a continuous nucleic acid chain

Dear all: I am facing a display issue in pymol. In my structure, there is a nucleic acid chain with some monomers which are modified nucleotides built in scketcher of ccp4 suite. However, When I showed the structure in pymol as cartoon, the nucleic acid chain was discontinuous where the monomer

Re: [ccp4bb] Trouble Refining Ligand in Phenix

Actually, that was the issue. I manually reset the occupancies of the problematic atoms in the PDB to unity. This solved my problem. Thanks to Nat and Tom. Best, Chris On 4/21/14, tom.p...@csiro.au wrote: > Hello Chris, > > This probably isn't your problem, but I once put some atoms into differ

Re: [ccp4bb] Non-catalytic Rossmann fold domain

DprA, from the Streptococcus pneumoniae transformasome, is one, I believe: http://www.ncbi.nlm.nih.gov/m/pubmed/22904190/ > On 22 Apr 2014, at 14:26, "Tanner, John J." wrote: > > Does anyone know of a protein that has a Rossmann dinucleotide binding domain > that does not participate in cofact

Re: [ccp4bb] Non-catalytic Rossmann fold domain

Dear Jack, In this recent review paper (http://www.biomedcentral.com/1472-6807/13/6), I read about non-catalytic Rossmannn fold proteins which include mitochondrial transcription factor B (sc-mtTFB) (http://www.ncbi.nlm.nih.gov/pubmed/12897151) and a t-RNA (1-methyladenosine) MTase from Sacchar

[ccp4bb] Tenure track position in Protein Chemistry, Leiden University, NL

Dear all, Leiden University, The Netherlands has a tenure track position available in its Protein Chemistry department. For details, please see the following site: http://werkenbij.leidenuniv.nl/vacatures/wetenschappelijke-functies/14-118-vacature-universiteit-leiden-tenure-track-position-in-pro

Re: [ccp4bb] Non-catalytic Rossmann fold domain

Hi Jack, my memory is a bit rusty but I think that the Gamma subunit of ATP synthase has a non-catalytic Rossmann fold that forms the foot of the central stalk with 2 other small subunits. Best wishes, Matt. On 2014-04-22 15:26, Tanner, John J. wrote: Does anyone know of a protein that h

[ccp4bb] Non-catalytic Rossmann fold domain

Does anyone know of a protein that has a Rossmann dinucleotide binding domain that does not participate in cofactor/substrate binding? Thanks. Jack Tanner John J. Tanner Professor of Biochemistry and Chemistry University of Missouri-Columbia 125 Chemistry Building Columbia, MO 65211 email: ta

Re: [ccp4bb] MIND in shelxd

Can be tricky - espec. since many MET have multiple conformations.. I set MIND to 2.5 but that is a guess. I use SHELX C/D/E to find some, get the hand, then give those PHASER-EP to refine and phase again and find minor sites Eleanor On 22 April 2014 07:41, Monica Mittal wrote: > Dear all

Re: [ccp4bb] Dehydration

Dear Yahui, I also suggest In-situ dehydration combined with in-situ diffraction . See paper below "Using high-throughput in situ plate screening to evaluate the effect of dehydration on protein crystals", Alice Douangamath et al, Acta Cryst. (2013). D69, 920–923 --

Re: [ccp4bb] Dehydration

one thing you can try and which we have used successfully (although not with an organic as the main precipitant) is too add more precipitant to the well and equilibrate for say one or two days. We often use LiCl salt as it is very soluble (you can make a 10 M solution). You can try adding to 1 M

Re: [ccp4bb] Dehydration

Dear Yahui, Your problem is quite common and very frustrating, I know. 1) Did you try to find new crystallisation conditions by re-screening using micro-seeds? 2) Did you try Additive Screens? 3) In-situ diffraction may also help you to have a feeling about the diffraction power of your cryst

Re: [ccp4bb] shelxd

I think what one uses will depend on what one expects to be in the structure and the resolution and the quality of their diffraction data. I usually start with 1.8 Å resolution data in case there is chance of having disulfides. Then 1.9, then 2.4, then 2.0, then 2.6, then 2.2, then 1.85, then

[ccp4bb] Dehydration

Dear all, Right now, we are try to crystallise an protein complex. By all kinds of efforts, the resolution of the crystal was about 8 angstrom. So we would like to try dehydration. The precipitant that our crystal grew was ethanol. Since the evaporation of the ethanol, our crystal is unstable at t

Re: [ccp4bb] shelxd

Dear Monica, if you are new to phasing I recommend you first use the ``standard'' values in shelx c/d/e, either using one of my tutorials or, even better, the GUI hkl2map, available at http://webapps.embl-hamburg.de/hkl2map/. If your native data are about 2A or better, and your structure is a pro

[ccp4bb] AW: [ccp4bb] coot problems to decrease R FREE

Dear Peter, First a common misconception: your goal should be to get the best possible fit of your model to your electron density maps. Rfree is only an indicator, telling you whether you are moving in the right direction. So in coot, you should look for places where your model does not fit the

[ccp4bb] shelxd

Dear all I am naive in phasing experiments. CAn anyone please guide how to do the following: In a S-SAD for *SHELXD* searches, try various high-resolution cutoffs for example 2.5 to 5 Å in steps of 0.1 Å. Based on these attempts, use a high-resolution cutoff at for example 3.8 Å for substructure