Towards automated crystallographic structure refinement with phenix.refine

phenix.refine is a program within the PHENIX package that supports crystallographic structure refinement against experimental data with a wide range of upper resolution limits using a large repertoire of model parameterizations. This paper presents an overview of the major phenix.refine features, with extensive literature references for readers interested in more detailed discussions of the methods

phenix.model_vs_data: a high-level tool for the calculation of crystallographic model and data statistics

Application of phenix.model_vs_data to the contents of the Protein Data Bank shows that the vast majority of deposited structures can be automatically analyzed to reproduce the reported quality statistics. However, the small fraction of structures that elude automated re-analysis highlight areas where new software developments can help retain valuable information for future analysis

Crystal Structures of Malonyl-Coenzyme A Decarboxylase Provide Insights into Its Catalytic Mechanism and Disease-Causing Mutations

Malonyl-coenzyme A decarboxylase (MCD) is found from bacteria to humans, has important roles in regulating fatty acid metabolism and food intake, and is an attractive target for drug discovery. We report here four crystal structures of MCD from human, Rhodopseudomonas palustris, Agrobacterium vitis, and Cupriavidus metallidurans at up to 2.3 Å resolution. The MCD monomer contains an N-terminal helical domain involved in oligomerization and a C-terminal catalytic domain. The four structures exhibit substantial differences in the organization of the helical domains and, consequently, the oligomeric states and intersubunit interfaces. Unexpectedly, the MCD catalytic domain is structurally homologous to those of the GCN5-related N-acetyltransferase superfamily, especially the curacin A polyketide synthase catalytic module, with a conserved His-Ser/Thr dyad important for catalysis. Our structures, along with mutagenesis and kinetic studies, provide a molecular basis for understanding pathogenic mutations and catalysis, as well as a template for structure-based drug design

Variable period undulator with tunable polarization

The proposed magnetic structure allows to control all the parameters of the sinusoidal magnetic field $B(s)=B_{0}·sin(2πs/λ_{U}+ϕ)$ of permanent magnet undulator: amplitude $B_0$, period length $λ_U$, and phase $ϕ$. The magnetic structure consists of diametrically magnetized cylindrical magnets at fixed positions. The field is adjusted by motorized rotation of each magnet. Tuning of radiated wavelength by changing the period length instead of field amplitude is more effective and results in a wider wavelength range and higher photon flux, especially for free electron lasers. Individual adjustment of the magnets allows for creating arbitrary shaped magnetic field and also for embedding other elements like phase shifters, dipoles, or multipole lenses into the undulator magnetic structure

Influence of Radiation Exposure on the FEL Performance at FLASH

FLASH has been operated as user facility for about 14 years. In this time, the total charge accelerated and transported through the FLASH1 undulator is around 35 Coulomb. Based on detailed monitoring of the radiation loss and reference measurements on degradation of the magnetic field of the undulator, we have performed simulations to study the change in FEL performance and first comparison of the simulations with the changes we observe during operation

An adaptive scheme for suppression of higher harmonics in an undulator

An undulator usually emits radiation at the energy of the fundamental wavelength and the higher harmonics at the same time. Likewise, monochromators with gratings or low-indexed crystals also transmit these higher harmonics with substantial efficiency. Most experiments, however, require a clean monochromatic spectrum and use mirrors or a detuning of the monochromator to suppress the higher harmonics in the spectrum. A quasi-periodic undulator is a well- established device which shifts the position of the higher harmonics to non-integer multiples of the fundamental and helps to improve the signal-to-background ratio in the measurement significantly.We have implemented a new alternative concept for suppression of higher harmonics which can be adapted on the fly during operation of the undulator. It is based on creating a distinct phase step in the center of the magnet structure which leads to a tailored distortion of the emitted spectrum. For that purpose, a permanent magnet phase shifter is embedded into the magnet structure of a planar hybrid undulator. We discuss the principle and technical implementation of this scheme, and present first experimental results

Permanent Magnet phase shifters for FLASH2020+ FEL

The development of a simple and compact permanent magnet (PM) phase shifter is presented in this paper. The design is based on four PM blocks per girder (8 PM blocks in total), and uses only one type PM block with horizontal magnetization and 15mm length. The magnetic field provides a net zero and second field integral and a phase integral of 2 · 10$^{–6}$ T$^2$m$^3$ for 60mm overall magnet length. The study of the numerical model with Radia shows that this design is mainly sensitive to angular magnetization errors. The correction strategy is based on pairing the PM blocks in order to cancel the sum of magnetization angle error, and the remaining magnetic field error is corrected with a stack of magic fingers located around the magnet. Finally, a prototype was built, and the magnetic measurements results are presented here

Properties of the Insertion Devices for PETRA III and its Extension

In 2007 and 2008, the PETRA ring at DESY was rebuilt from a booster for HERA to a low emittance synchrotron radiation source, called PETRA III. During the reconstruction for one eighth of the storage ring, the FODO lattice was replaced by nine double bent achromat cells, now accommodating insertion devices for 14 independent beamlines. Besides the 2 m long standard undulators U29 and U32, several special IDs of up to 5 m length have been installed to meet the experimental requests for high energy X-rays, elliptically polarized light, and a higher degree of coherence. This article will give an overview over the key parameters like the spectral properties, the brilliance and the power density of the current undulators installed at PETRA III