Experimental phasing with SHELXC/D/E: combining chain tracing with density modification

Experimental phasing with SHELXC/D/E has been enhanced by the incorporation of main-chain tracing into the iterative density modification; this also provides a simple and effective way of exploiting noncrystallographic symmetry

Rapid chain tracing of polypeptide backbones in electron-density maps

A method for rapid chain tracing of polypeptide backbones at moderate resolution is presented

Rapid model building of β-sheets in electron-density maps

A method for rapid model building of β-sheets at moderate resolution is presented

Revisiting the planarity of nucleic acid bases: Pyramidilization at glycosidic nitrogen in purine bases is modulated by orientation of glycosidic torsion

We describe a novel, fundamental property of nucleobase structure, namely, pyramidilization at the N1/9 sites of purine and pyrimidine bases. Through a combined analyses of ultra-high-resolution X-ray structures of both oligonucleotides extracted from the Nucleic Acid Database and isolated nucleotides and nucleosides from the Cambridge Structural Database, together with a series of quantum chemical calculations, molecular dynamics (MD) simulations, and published solution nuclear magnetic resonance (NMR) data, we show that pyramidilization at the glycosidic nitrogen is an intrinsic property. This property is common to isolated nucleosides and nucleotides as well as oligonucleotides—it is also common to both RNA and DNA. Our analysis suggests that pyramidilization at N1/9 sites depends in a systematic way on the local structure of the nucleoside. Of note, the pyramidilization undergoes stereo-inversion upon reorientation of the glycosidic bond. The extent of the pyramidilization is further modulated by the conformation of the sugar ring. The observed pyramidilization is more pronounced for purine bases, while for pyrimidines it is negligible. We discuss how the assumption of nucleic acid base planarity can lead to systematic errors in determining the conformation of nucleotides from experimental data and from unconstrained MD simulations

Organic-soluble optically pure anionic metal complexes PPh4[M-III(S,S-EDDS)]center dot 2H(2)O (M = Fe, Co, Cr)

The first organic-soluble, optically and diastereomerically pure EDDS metal complexes have been synthesised. A number of synthetic approaches were attempted, but finally the tetraphenylphosphonium series emerged as providing readily accessible compounds of trivalent Cr, Fe and Co in reasonable yields via the silver salts without the need to perform ion-exchange chromatography. The species PPh4[M-III(S,S-EDDS)] are very soluble in methanol, acetonitrile and even THF but isolation was facilitated by addition of stoichiometric water giving the highly crystalline but still conveniently soluble title compounds. The structures of the three isomorphous crystals comprise H2O-bridged extended hydrogen bonded structures with large channels occupied by the counterion molecules. The magnetic properties and circular dichroism spectra are reported along with comparative data for water-soluble NH4[Fe-III(S,S-EDDS)]. Phase purity (and hence diastereomeric purity) in the paramagnetic systems is assessed through powder XRD. The practical utility of this type of compound was confirmed by optical resolution of (+/-)-[Ru-II(bpy)(3)]Cl-2