Re: [ccp4bb] NCS edits in COOT

> Q4. Is there another option, not COOT? > > > > > > > > > > > Dr Felix Frolow > Professor of Structural Biology andBiotechnology, > Department of MolecularMicrobiology and Biotechnology > Tel Aviv University 69978, Israel > > Acta Crystallogra

Re: [ccp4bb] repulsive effects of arginine

In 3U9C we observed even 6 arginines (residues A278, A280 and A306 plus symmetry mates of chain B) mediating a crystalline contact by pi/pi stacking. We called this motif an "arginine zipper" (see Fig. 5 in dx.doi.org/10.1107/S0907444912016587). Karsten Niefind An example of pi-p

[ccp4bb] Screening a protein surface for interaction sites

tes with potential ligands of any kind (preferentially other proteins and peptides, but also nucleic acids or small metabolites and with emphasis on "potential", i.e. if no concrete ligand is known)? Thanks for any help from Karsten Niefind ------- Karsten Niefi

Re: [ccp4bb] NADP binding protein without Rossmann fold.

/pubmed/20887732) bind NAD(P) and have an (alpha/beta)8 barrel motif. Best wishes, Karsten Niefind - Karsten Niefind, PhD University of Cologne Department of Chemistry Otto-Fischer-Str. 12-14 D-50674 Cologne Tel.: +49 (0)221 4706444 Fax: +49 (0)221 4703244

Re: [ccp4bb] asking for a reference for cacodylate decomposition in protein crystals upon X-ray exposure

ncerely, > Tanya > Dear Tanya, cacodylate can be attacked by nucleophilic side chains and can form covalent adducts, e.g.: http://www.jbc.org/content/278/3/2008.long Good luck, Karsten --- Karsten Niefind University of Cologne Department of Chemistry Institute

Re: [ccp4bb] question about a dataset with pseudotranslational symmetry

Twinning and intensity statistics summary (acentric data): > Statistics independent of twin laws > /^2 : 2.568 > ^2/ : 0.728 > <|E^2-1|> : 0.850 > <|L|>, : 0.490, 0.323 > Multivariate Z score L-test: 0.686 > > ------- > > Jiyuan Ke, Ph

Re: [ccp4bb] is my crystal twinned or not?

d strategy to come to a better defined electron density and structure. Or was it a case of "over-twinning"? Many thanks in advance and best wishes from Karsten - Dr. Karsten Niefind University of Cologne Department of Chemistry - Institute of Biochemistry Zuel

Re: [ccp4bb] structure (factor) amplitude

here |F| is introduced they > define it as: 'the most > important quantity derived from the intensities is the structure factor > modulus (structure > amplitude). (Italics are theirs, not mine). > Sue Dear experts, what about the phases? Should they termed "structure phases"? Karsten Niefind

Re: [ccp4bb] meaning of R free of perfect twin

Am 5 Dec 2008 um 13:50 hat Agnieszka Kiliszek geschrieben: > Hi, > > What is the meaning of R free of perfect twin? Shelxl counts it but it > seems that the R f is no longer independent. > > Aga Dear Aga, I also had this problem, however with Refmac5.5. My solution was to use the CNS script

Re: [ccp4bb] Anion binding sites in proteins

Dear Albert, please have a look at dx.doi.org/10.1007/s11010-008-9826-1 Good luck! Karsten --- Dr. Karsten Niefind Institute of Biochemistry Department of Chemistry University of Cologne Zuelpicher Strasse 47 D-50674 Cologne tel.: +49/221/470-6444 fax

[ccp4bb] Programs for analysing the "drugability" of a small-molecule binding pocket

Dear colleagues, I am looking for a computational method to assess reliably the "drugability" of a small- molecule binding pocket (volume, surface, interaction potential etc.) on a protein surface. Any recommandations and experiences are welcome! Many thanks in advance! Karst