[ccp4bb] add ligand solution onto drop directly SUMMARY

Thanks for the responses. Yes, my crystal did survive and I can see density for my ligand. Summary: 1. If the crystal survives, it’s fine. These are just different ways of exposing the crystal to the ligand and do what works. The only issue will be if you don’t see electron density for the ligand

Re: [ccp4bb] CCP4BB Digest - 24 Jan 2017 to 25 Jan 2017 (#2017-26)

On Thursday, 26 January 2017 11:03:12 PM Claire Smith wrote: > Hello, > > I would like to ask a question related to a recent thread regarding > bad/missing density. > > I have used SAD to solve the structure of a protein at about 2.6Å > resolution. Phenix build a good portion of it (about 50%)

Re: [ccp4bb] CCP4BB Digest - 24 Jan 2017 to 25 Jan 2017 (#2017-26)

Hello, I would like to ask a question related to a recent thread regarding bad/missing density. I have used SAD to solve the structure of a protein at about 2.6Å resolution. Phenix build a good portion of it (about 50%) and the density in this region is good. However, we cannot see ther rest

[ccp4bb] TLSMD server down with disk problems

The TLSMD server is suffering from hardware problems. It is unclear how long it will take to fix this, or whether the whole machine will need to be replaced. I'd love it if someone would undertake to run a mirror or equivalent server, but as it stands I think you're out of luck until I can round

[ccp4bb] Experimental Postdoctoral Position in High Throughput Small Molecule Ligand Screening

Outstanding postdoctoral applicants are sought with the following qualifications to work with Dr. Jeffrey Skolnick in the Center for the Study of Systems Biology in the School of Biological Sciences at the Georgia Institute of Technology: • Extensive experience in enzyme kinetics

[ccp4bb] TLSMD Server ?

Hi CCP4BB, Somebody know what happen with the TLSDM server at http://skuld.bmsc.washington.edu/~tlsmd/ It has been refusing connections for already two days? Perhaps a mirror exists somewhere ? Best Carlos -- Carlos CONTRERAS MARTEL, Ph.D. (CR1 CNRS)

[ccp4bb] 5th Banff Meeting on Structural Dynamics, 19th Febr. - 22nd Febr. 2017 / approaching deadline for late abstract submission for posters

Dear all, Please mind the approaching deadline (= 30th January 2017) for abstract submission regarding posters to be presented at the 5th Banff Meeting on Structural Dynamics https://banff2017.desy.de/ Best regards, Irmtraud Kleine Assistant to Professor Chapman Deutsches

Re: [ccp4bb] wavelength dependence of intensities

Dear Tim, That is described by the Laue interference function. The crystal diffracts in Bragg directions (reflections) at small deviations of the Bragg angle and in a small solid angle. They depend on lambda and lambda^2 respectively, and integration over these angles brings a factor

Re: [ccp4bb] glycosylated density blob?

You mentioned that you have PMSF in your crystallization condition…and PMSF does modify serines. Best regards, Z *** Zachary A. Wood, Ph.D. Associate Professor Department of Biochemistry & Molecular Biology University of

[ccp4bb] wavelength dependence of intensities

Dear all, according to Carmelo Giacovazzo's textbook (eq. 3.41 in the 1st edition), the diffraction intensity I(hkl) scales with the wavelength cubed (lambda^3). 1) is there an easy rationale for this dependency? 2) does it hold over a wide range of energies? 3) does this also hold for neutrons

Re: [ccp4bb] glycosylated density blob?

well yes, looks like a glycosylation to me too. However, at 2.75Å resolution I think it will be impossible to know which one from the density alone. Perhaps mass spectroscopy can give a clue? Or get clues from what is known about your protein and your expression system. Mark J van Raaij Dpto de

Re: [ccp4bb] Bad density for chains

You could try the diffraction anisotropy server: http://services.mbi.ucla.edu/anisoscale/. Sometimes it helps maps become more interpretable. Ben On 26 Jan 2017, at 14:11, Pooja Kesari wrote: We have a 2.6 A structure showing four chains in an asymmetric unit.

[ccp4bb] AW: [ccp4bb] Bad density for chains

Dear Pooja, A few remarks: -Matthews does not show 4 chains in the asymmetric unit, it suggests 4 chains. However, in reality it can be more or less chains, although rare, 75% solvent (2 chains) is not unheard of. -An initial Rfree of 38% is ok, 32% after refinement is a bit

Re: [ccp4bb] Bad density for chains

Well - first Solvent content.. 1) there could be 4 molecules, or 3, or 2.. Solvent content varies a lot as you know. Is there reasonable density for parts of all the chains? 2) Does the MR search clearly show 4 molecules? ie improvement in scores with extra molecules? 3) Have you checked for

Re: [ccp4bb] Bad density for chains

Hi, assuming you've exhausted modeling choices and applied proper refinement strategies, after all Rree=32% is not unheard of at 2.6A resolution (which actually may be even worse than 2.6A if data set is not 100% complete). Have a look at R-factors of models in PDB with data resolution around

Re: [ccp4bb] Bad density for chains

We have a 2.6 A structure showing four chains in an asymmetric unit. Our protein is 360 residues around 40 kDa . Mattews shows four chain in an assymetric unit (solvent 49% mattews coeff 2.44). The template has about 60% homologous with our protein. The molecular replacement against this template

Re: [ccp4bb] Bad density for chains

This is a bit too vague to help much. How did you solve the structure? Eleanor On 26 January 2017 at 03:50, Pooja Kesari wrote: > Dear All, > Thank you all for reply. > > We have checked the data for twinning. > Our protein is 360 residues around 40 kDa protein. > We have