Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix

Recent developments in the Phenix software package are described in the context of macromolecular structure determination using X-rays, neutrons and electrons.

Deriving and refining atomic models in crystallography and cryo-EM: the latest Phenix tools to facilitate structure analysis

In structural biology, deriving and refining atomic models into maps obtained from X-ray crystallography or cryo electron microscopy (cryo-EM) is essential for the detailed interpretation of a structure and its functional implications through interactions so that for example hydrogen bonds, drug specificity and associated molecular mechanisms can be analysed. This commentary summarizes the latest features of the Phenix software and also highlights the fact that cryo-EM increasingly contributes to data depositions in the PDB and EMDB.

Flexible workflows for on-the-fly electron-microscopy single-particle image processing using Scipion

The Scipion framework allows very flexible image-processing workflows to be generated and employed at electron-microscopy facilities, such that image acquisition can be monitored and possible problems detected, thereby enabling early decisions to be made on the fly. The streaming workflow can be very simple or extended, permitting the data resolution and heterogeneity to be estimated and adapted to the desire of the user and the microscope operator.

Structural comparison of protiated, H/D-exchanged and deuterated human carbonic anhydrase IX

In this work, the X-ray crystal structures of four different deuterium-labelled versions of a surface variant of human carbonic anhydrase IX are compared and discussed. The results show that the overall structure and active-site organization of each version are essentially the same, paving the way for future neutron protein crystallography studies.

Comparison of a retroviral protease in monomeric and dimeric states

Mason–Pfizer monkey virus protease has been crystallized in a dimeric form using nearly the same conditions as those that yielded crystals of the monomeric form. A comparison of the structures of the two states highlights the conformational changes accompanying retropepsin dimerization.

The flavin mononucleotide cofactor in α-hydroxyacid oxidases exerts its electrophilic/nucleophilic duality in control of the substrate-oxidation level

Structural and enzymological explorations of p-hydroxy-mandelate oxidase and its mutants uncover an unprecedented electrophilic/nucleophilic duality for the flavin mononucleotide cofactor as well as an intramolecular disproportionation mechanism for an oxidative decarboxylation reaction.

Structure determination of the nucleosome core particle by selenium SAD phasing

The structure of the human nucleosome core particle was solved by selenium SAD phasing. The present study demonstrates that nucleosome structures can be readily determined by experimental phasing and provides a method for solving nucleosome structures by X-ray crystallography in cases where the phase information is difficult to obtain by molecular replacement.

Well-based crystallization of lipidic cubic phase microcrystals for serial X-ray crystallography experiments

A novel method is presented to screen for suitable crystallization conditions and produce large amounts of microcrystals of membrane proteins in lipidic cubic phase for serial crystallography experiments.