Re: [ccp4bb] partial density

Dear Kumar, This is perfectly normal. Long and flexible side chains e.g. lysines, facing the solvent move around and have weak electron density. In fact, I have not seen a structure where this is not the case. If you get strong Fo-Fc density back, I would fit the side chains and not worry about

Re: [ccp4bb] xds and cell refinement in cP

Hi Jan, Always worth a try is to process the data in P1 then assigning the symmetry in CORRECT - that way the cell constants can refine to what they want to. It also means you can check that the symmetry actually is cubic. For the majority of data sets in my experience it makes little difference

Re: [ccp4bb] Nobel prize for chemistry 2009

A Leslie wrote: BB members may be interested to know that the 2009 Nobel prize for chemistry has been awarded to Venki Ramakrishnan, Tom Steitz and Ada Yonath for their structural work on the bacterial ribosome. FYI:

[ccp4bb] Beamtime at X06SA, SLS, PSI - deadline: 15th October

= SYNCHROTRON BEAM TIME FOR MACROMOLECULAR CRYSTALLOGRAPHY AT THE UNDULATOR BEAMLINE X06SA AT SLS FROM JANUARY TO APRIL 2010 = - Automatic sample changer (IRELEC CATS)

Re: [ccp4bb] Nobel prize for chemistry 2009

The patent #7504486 you cited actually only covers 'A method of growing a crystal of a 50S ribosomal subunit from Haloarcula marismortui', i.e. the crystallisation method for the 50S subunit from this single organism (from my school Latin I deduce 'haloarcula' = 'small box of salt' and

[ccp4bb] cif file for NAD

Dear All, I would like to request to send me a working and correct cif file for NAD. I obtained the same from Prodrg and ebi. But seems to have an issues around O1N-PN-O2N O3-PN-O5. Thanks With best regards Rajesh Rajesh Kumar Singh, PhD Biochemical Engg. Group Chemical Engg. Division Dr. Homi

[ccp4bb] temperature factors, mosaicity and wilson plot

Hi, I recently solved the structure of a mutant protein that contains a single amino acid substitution. Here are some data about the mutant: resolution: 2.65 A completeness: 99.9 % (100.0 %) Rwork/free: 22.3/27.8 % Rsym 15.6 (47.7) % avg. mosaicity: 0.48° now whats confusing me: Wilson

Re: [ccp4bb] mammalian cell culture on IMAC

Dear All, When mammalian cell culture is being loaded to GE HisTrap resin Ni ions are being stripped off the resin, at least in my hands. Did any of you have similar experience and if so what kind of work-around was found? Volume is fairly large (3L) and concentration/dialysis have proven to

Re: [ccp4bb] mammalian cell culture on IMAC

In case of cell lysates this may be a good idea since you can adjust the salt concentration in your sample. In case of secreted proteins it is probably not so good since the media contains ~150 mM NaCl. In my case this salt prevents protein from bindinq to Q column. Thank you anyway.

Re: [ccp4bb] mammalian cell culture on IMAC

I had exactly the same problem. You should switch to Talon matrix (Clontech). The cobalt ion is bound more tightly so stripping is dramatically reduced. Furthermore, the Talon matrix is more specific (then Ni Sepharose) for your His-tagged protein, so you have less contaminants. I load two to

Re: [ccp4bb] mammalian cell culture on IMAC

We tried that trick, which works amazingly well in insect cells, in mammalian media, and it fails. It will depend on the exact media, obviously. Engin On 10/8/09 1:50 PM, Matthew Franklin wrote: The trick we used at Genentech (which I'm still using) was for secreted insect cell proteins, but

[ccp4bb] Coot and X11

I am trying to install the pre-compiled version of Coot on OSX 10.5.4. I downloaded the program from Bill Scott's website. When I try to run Coot, it complains about the wrong version of libXdamage.1.dylib. It needs 3.0 and I have 2.0. I currently have Xcode 3.0 and Xwindows 2.0 installed. How

[ccp4bb] mammalian cell culture on IMAC

This article discusses this effect in E. coli lysates. Please let us know if you find something that works well with insect/mammalian lysates or secreted proteins! Enabling IMAC purification of low abundance recombinant proteins from E. coli lysates

Re: [ccp4bb] cif file for NAD

Dear RajeshCould you please try the attached dictionary. Please let me know if it still has a problem.What are the issues around O1N-PN-O2n and O3N-PN-O5?regardsGarib nad_exp.cif Description: Binary data On 8 Oct 2009, at 15:11, RK Singh wrote:Dear All,I would like to request to send me a working

[ccp4bb] Question about the covalent Link between PLP Lysine

Dear All, I’m currently refining the structure (2.0 A) with a cofactor PLP. The PLP density is clearly indicates lysine residue is covalently bound with PLP cofactor. But I don’t know how to link the cofactor and lysine residue for further refinement. Any suggestions on how to create the link