[ccp4bb] Conference on Methods and applications in the frontier between MX and CryoEM.

Dear all, It seems that I have sent an email with large image. Please discard that email. Here is an email I wanted to send. It is an announce of the conference on cryo-EM and crystallography in Barcelona. I think it is going to be an exciting conference with very good set of speakers. Here is

Re: [ccp4bb] Glycoprotein expression question

Hi Bernhard, I guess you knew all these and is really asking for people's experience, but please excuse me to start from the theory: N-glycans in eukaryotes are known to be involved in glycoprotein folding in the ER. They allow the nascent protein to get into the calnexin/calreticulin cycle

[ccp4bb] Postdoctoral Positions at Brookhaven National Laboratory USA

Dear Colleagues, The Quantitative Plant Science Initiative at Brookhaven National Laboratory in New York is seeking exceptional candidates for two post-doctorate associate positions with strong backgrounds in structural biology. The successful candidates will join a multi-disciplinary team

Re: [ccp4bb] High Rfree: Phasing issue or partial crystal disorder

HOW sure are you of the spacegroup? The only difference between I4 ans I41 absences is that l=2n is absent for I4, l=4n for I 41. If you have the wrong choice half your symmetry equiv molecules will be corret but not the others.. Getting the screw axis wrong is a good way to get a reasonable but

[ccp4bb] 2 Wellcome Trust funded Post-Doc positions (4y) available in Berger group, University of Bristol, UK

Dear CCP4bb and CCPEM members, Up to two Research Associate positions in cellular structural biology of transcription factors are available immediately in the Berger lab, University of Bristol UK, funded by the Wellcome Trust. As part of a dynamic interdisciplinary team, the Research Associates

[ccp4bb] Fwd: Re: [ccp4bb] Glycoprotein expression question

Hi Savvas, Thank you for kindly pointing to our review. Bernhard, in my experience your case is a rare exception rather than the rule, so indeed lucky. Adrian summarised very nicely the wide impact glycans may have on folding, trafficking and/or function. To keep things simple, there is no need

Re: [ccp4bb] High Rfree: Phasing issue or partial crystal disorder

Hi, Sometimes automated model building needs more manual intervention than one might expect, although it sounds like you've already carefully inspected the "good" regions. Could you use a model of the N-ter (from a homolog) simply to create a solvent envelope, then see if solvent flattening

Re: [ccp4bb] High Rfree: Phasing issue or partial crystal disorder

Dear Mark, Thanks for your reply. I have already tried P1 SG (we do have 360 degree data) and Zanuda server without success. I do now have crystals in different conditions (and visually they are of different shape). In parallel I am trying heavy metal soaking and hope one of the strategy will

Re: [ccp4bb] Coot Find Ligand Places Ligand In Density Outside Where Model Is Built

On 12/04/17 00:31, Roger Shek wrote: Does anyone know why Coot is placing ligand outside the electron density where my model is built. I have put the cursor to where I want it to search, but when it fits, it places the ligand in the equivalent spot, but outside the model and not where the

Re: [ccp4bb] Glycoprotein expression question

Dear Bernhard Our campaigns over the years aiming to produce mammalian cytokines and the ectodomains of cytokine receptors via eukaryotic expression systems (mainly in several HEK293 flavors) for structural biology, have taught us that the N-linked glycosylation issue remains a very empirical

Re: [ccp4bb] High Rfree: Phasing issue or partial crystal disorder

Dear Pravin, we've had a couple of these unfortunately, in our case the only solution has been to find alternative crystal forms. Or several crystal forms in which different domains are disordered, but allowing to make a composite, complete structure for interpretation. Your N-terminal domain

Re: [ccp4bb] Glycoprotein expression question

Good morning, Bernhard, I do not think that you had pure luck (though serendipity helps a lot). You said that the PNGaseF treated protein was indeed stable, that was already a good hint. In my little experience with N- and O-glycoproteins, with not a high percentage of sugar content, I saw a

Re: [ccp4bb] Glycoprotein expression question

I think it completely depends on the protein: in some proteins, they are required for folding; in some (eg Fcs), they are not required for folding but for function); in some, some of them are required and others not; in some they are required _during_ folding, but afterwards they can be removed

Re: [ccp4bb] Glycoprotein expression question

We had experience with a relatively small glycoprotein - when glycosylation sites were deleted, solubility went drastically down - we could not express soluble any more. Back to eukaryotic expression system which worked. So may be you were really lucky. Jan On Tue, Apr 11, 2017 at 10:34 PM,

Re: [ccp4bb] electronic lab notebook suggestions

Dear Markus, For the last years I have been using LabArchives, since I got an account for "free" with my Graphpad Prism license. I've been mostly happy with it. It can automatically upload attachments from a watched folder, and integrates with some useful software such as Prism and chemdoodle.