Re: [ccp4bb] Dimer in SDS-PAGE

Dear all, this all depends on the protein: some 7TM proteins are nicely resolved as 1 band of ~the expected size upon 5 min sonication - 5 min 95 °c - 5 min sonication in sample buffers containing 2 M urea Others still gave mono- & dimers The treatment above also wored for a pentameric 4TM

Re: [ccp4bb] Twinning and R-Free

Hi Alun and Kay, PDB_REDO does some more extended twinning testing with among others Phaser, so it would be worthwhile to have a look at that. On the server it refuses to do twinned refinement if there is no clear indication of twinning even if the user assumed twinning before. The fact the

Re: [ccp4bb] Twinning and R-Free

Hi Alun, 1. What does phenix.xtriage think of the dataset? 2. What kind of redundancy do you have in the dataset? 3. Sometimes with a large crystal and a small beam the twin fraction varies as you rotate the crystal and illuminate different parts of the crystal (which can have different twin

Re: [ccp4bb] Dimer in SDS-PAGE

Dear Bert You made the comment a few weeks ago not to boil helical membrane proteins for SDS-PAGE. Could i please ask, does this also apply to type I membrane proteins that only have a single a-helix, or is it just membrane proteins that are predominantly helical? Thanks Rich On 22 February 2017

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

We have seen a similar thing once, where we obtained proteins crystals simply by dehydration of the drop: Sharpe, M. L., Baker, E. N., and Lott, J. S. (2005) Crystallization of a protein using dehydration without a precipitant. Acta Crystallogr Sect F Struct Biol Cryst Commun 61, 565–568.

[ccp4bb] Formulatrix Position Announcement: Product Manager for Protein Crystallization

Dear colleagues, I would like to advertise a new position that is available at Formulatrix for a "Product Manager for Protein Crystallization". This exciting position will enable you to define the roadmap of our products around protein crystallization. The details of the project are as defined

Re: [ccp4bb] Twinning and R-Free

Hi Alun, that's difficult to understand for me. It is my understanding that for an imperfect model, refmac will indicate a twin fraction >0 even if in reality it is 0. But alpha=0.372 sounds too high for that. My questions would be - a) is it a single dataset, or did you merge ? If the latter,

[ccp4bb] Twinning and R-Free

Hi Everyone, I have a (2.5 - 2.3 Angstroms) data set the process as I4 or I222. Aimless indicates twinning in both space groups and all the lower symmetry space groups consistent with the reduced cell. Molecular replacement works in I4 but not I222 etc. I can see new density for a ligand we

Re: [ccp4bb] How to refine this needle crystal of membrane complex?

For historical perspective: Molecular structure determination by electron microscopy of unstained crystalline specimens PNT Unwin, R Henderson - Journal of molecular biology, 1975 http://www.sciencedirect.com/science/article/pii/0022283675902120 From:

Re: [ccp4bb] How to refine this needle crystal of membrane complex?

There are now quite a few structures solved by ED of 3D crystals, esp by Tamir Gonen's group here at Janelia, and a quick count in the pdb yields ~15 3D-crystal ED structures, some of which are not released. They're getting better at it all the time. I guess the news has not spread as much as I

Re: [ccp4bb] How to refine this needle crystal of membrane complex?

Dear Jacob, dear TO, (I have wondered what can be 'micro' about diffraction - would you know?) it would be very exciting to get the structure by electron diffraction - as much as I know it would be the first new structure solved from a 3D crystal with electron radiation in the PDB. You would

[ccp4bb] Message from the British Biophysical Society

REGISTRATION IS NOW OPEN for the IUPAB/EBSA/BBS/IoP Congress in Edinburgh, 16 - 20th July 2017 (http://www.iupab2017.org/). Venki Ramakrishnan is presenting the opening Plenary Lecture and Bob Lewkowitz the closing Plenary Lecture. Chris Dobson gives a Public Engagement Lecture on the first

[ccp4bb] OPEN POST-DOCTORAL AND RESEARCH TECH POSITIONS IN STRUCTURAL BIOLOGY AND HIV AT FRED HUTCH, SEATTLE

Postdoc - http://www.fredhutch.org/job/9073 Research Tech - http://www.fredhutch.org/job/9072 Overview The Stamatatos lab, within the Vaccine and Infectious Disease Division, works towards the development of a safe and effective vaccine against HIV-1. Our major emphasis is the design of protein

Re: [ccp4bb] ANODE anomalous map in pymol

Deart Tim and Kamel, Thank you for your valuable advice. As Tim pointed out, the Shelx2map worked perfectly fine, and these are indeed very useful tools for anyone who is moving the map from the Shelx to pymol or CCP4. Yes, i did try the COOT exported map extension to .ccp4, but it did not work

Re: [ccp4bb] ANODE anomalous map in pymol

Hi Appu, Did you change the file extension of the exported map extension to .ccp4 (instead of .map)? That worked for me. Cheers Kamel -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Paul Emsley Sent: 28 February 2017 22:57 To: ccp4bb Subject:

[ccp4bb] CCP-EM Icknield Workshop for High Resolution Model Building - 2017

Dear all, We are proud to announce the 2017 Icknield Workshop. This course is aimed at structural biologists with high resolution EM maps ready for / in the process of modelling building and refinement. This three day course will host some of the leading software developers and provide ample

[ccp4bb] Automated pipelines for compound and fragment screening in Grenoble

Automated pipelines for compound and fragment screening in Grenoble The EMBL Grenoble, the ESRF and the iNEXT consortium are jointly offering access to automated pipelines for compound and fragment screening based on the CrystalDirect* technology and the MASSIF** beamlines. Access to these

[ccp4bb] West-Life Survey

Dear colleague, West-Life is an electronic infrastructure initiative (Virtual Research Environment, VRE) to support the use and analysis of structural biology data using advanced computational methods. We are now carrying out a survey to collect information that will guide our efforts to