BL03HB: a Laue microdiffraction beamline for both protein crystallography and materials science at SSRF

A Laue microdiffraction beamline(BL03HB) was constructed at the Shanghai Synchrotron Radiation Facility(SSRF).This beamline features two consecutive focusing points in two different sectors within its end station, the first dedicated to protein crystallography and the other tailored to materials science applications. Based on a superbend dipole magnet with a magnetic field of 2.29 T, a two-stage focusing design was implemented with two sets of Kirkpatrick-Baez mirrors to achieve a micro white beam as small as 4.2 μ m ×4.3 μ m at the first sector and 0.9 μ m ×1.3 μ m at the second sector in the standard beamline operation mode at SSRF. The X-ray microbeam in the two sectors can be easily switched between monochromatic and white beams by moving a four-bounce monochromator in or out of the light path, respectively. In the protein crystallography sector, white-beam Laue microdiffraction was demonstrated to successfully determine the structure of protein crystals from only a few images of diffraction data collected by a Pilatus 2 M area detector. In the materials science sector,the white-beam Laue diffraction was collected in a reflection geometry using another Pilatus 2 M area detector, which could map the microstructural distribution on the sample surface by scanning the samples. In general, the BL03HB beamline promotes the application of Laue microdiffraction in both protein crystallography and materials science. This paper presents a comprehensive overview of the BL03HB beamline, end station, and the first commission results.

BL02U1:the relocated macromolecular crystallography beamline at the Shanghai Synchrotron Radiation Facility

Macromolecular crystallography beamline BL17U1 at the Shanghai Synchrotron Radiation Facility has been relocated,upgraded,and given a new ID(BL02U1).It now delivers X-rays in the energy range of 6–16 keV,with a focused beam of 11.6μm×4.8μm and photon flux greater than 1012 phs/s.The high credibility and stability of the beam and good timing synchronization of the equipment significantly improve the experimental efficiency.Since June 2021,when it officially opened to users,over 4200 h of beamtime have been provided to over 200 research groups to collect data at the beamline.Its good performance and stable operation have led to the resolution of several structures based on data collected at the beamline.

The protein complex crystallography beamline(BL19U1)at the Shanghai Synchrotron Radiation Facility

The protein complex crystallographic beamline BL19U1 at the Shanghai Synchrotron Radiation Facility is one of the five beamlines dedicated to protein sciences operated by National Facility for Protein Science(Shanghai,China).The beamline,which features a small-gap invacuum undulator,has been officially open to users since March 2015.This beamline delivers X-ray in the energy range 7–15 keV.With its high flux,low divergence beam and a large active area detector,BL19U1 is designed for proteins with large molecular weight and large crystallographic unit cell dimensions.Good performance and stable operation of the beamline have allowed the number of Protein Data Bank(PDB)depositions and the number of articles published based on data collected at this beamline to increase steadily.To date,over 300 research groups have collected data at the beamline.More than 600 PDB entries have been deposited at the PDB(www.pdb.org).More than 300 papers have been published that include data collected at the beamline,including 21 research articles published in the top-level journals Cell,Nature,and Science.

Upgrade of macromolecular crystallography beamline BL17U1at SSRF

Beamline BL17 U1 at Shanghai Synchrotron Radiation Facility is an energy-tunable macromolecular crystallography beamline that has been in user operation since 2009. Growing demand from the user community for a small beam and related experimental methods have motivated upgrades of the devices in the endstation.Minibeam modes have already been developed for operation. A self-integrated diffractometer reduces the sphere of confusion of the rotatory axis to 1μm. The new diffractometer is equipped with an upgraded on-axis viewing system that can improve the resolving power. Additionally,the area detector was also upgraded to the newest generation of detectors, the EIGER X 16 M, which can collect data at 133 Hz. After these upgrades, the endstation became virtually new. This paper covers the upgrade of the endstation devices and gives the first data collection results.

Microstructure,crystallography and nucleation mechanism of NANOBAIN steel

The microstructure of bainite ferrite in NANOBAIN steel transformed at different temperatures was investigated by scanning electron microscopy, transmission electron microscopy, electron back-scattered diffraction, and vickers hardness tester in detail. It is found that the average width of bainitic ferrite （BF） plates can be refined to be thinner with the reduction of temperature （473-573 K）, and the bainitic ferrite plates can reach up to 20-74 nm at 473 K. Crystallographic analysis reveals that the bainitic ferrite laths are close to the Nishiyama-Wasserman orientation relationship with their parent austenite. Temperature shows a significant effect on the variant selection, and a decrease in temperature generally weakens the variant selection. Thermodynamic analyses indicates that the Lacher, Fowler and Guggenheim （LFG） model is more suitable than the Kaufman, Radcliffe and Cohen （KRC） model dealing with NANOBAIN steel at a low temperature range. The free energy change △G^γ→BF is about -1500 J.mol^-1 at 473 K, which indicates that nucleation in NANOBAIN steel is the shear mechanism. Finally, the formation of carbon poor regions is thermodynamically possible, and the existence of carbon poor regions can greatly increase the possibility of the shear mechanism.

Crystallography of Zr poisoning of Al-Ti-B grain refinement using edge-to-edge matching model

The mechanism of zirconium poisoning on the grain-refining efficiency of an Al-Ti-B based grain refiner was studied. The experiment was conducted by melting Al-5Ti-1B and Al-3Zr master alloys together. The edge-to-edge matching model was used to investigate and compare the orientation relationships between the binary intermetallic compounds present in the Al-Ti-B-Zr system. The results show that the poisoning effect probably results from the combination of Al3 Zr with Al3 Ti and the decreased amount of Ti solute, for Al3 Ti particles have good crystallographic relationships with Al3 Zr. Totally six orientation relationships may present between them, while they play vital roles in grain refinement. TiB2 particles appear to remain unchanged because of a bit large misfit. Only one orientation relationship may present between them to prevent Al3 Zr phase from forming on the surface of TiB2, though TiB2 is agglomerated. The theoretical calculation agrees well with the experimental results. The edge-to-edge matching model is proved to be a useful tool for discovering the orientation relationships between phases.

Effect of nano-sized precipitates on the crystallography of ferrite in high-strength strip steel

For strip steel with the thickness of 1.6 ram, the yield and tensile strengths as high as 760 and 850 MPa, respectively, were achieved using the compact strip production technology. Precipitates in the steel were characterized by scanning and transmission electron microscopy to elucidate the strengthening mechanism. In addition, intragranular misorientation, Kernel average misorientafion, and stored energy were measured using electron backscatter diffraction for crystallographic analysis of ferrite grains containing precipitates and their neighbors without precipitates. It is found that precipitates in specimens primarily consist of TiC and Ti4CzS2. Ferrite grains containing pre- cipitates exhibit the high Taylor factor as well as the crystallographic orientations with {012}, {011}, {112}, or {221} plane parallel to the rolling plane. Compared with the intragranular orientation of adjoining grains, the intragranular misorientation of grains containing precipi- tates fluctuates more frequently and more mildly as a function of distance. Moreover, the precipitates can induce ferrite grains to store a rela- tively large amount of energy. These results suggest that a correlation exists between precipitation in ferrite grains and grain crystallographic properties.

A revised version of the program VEC (visual computing in electron crystallography)

The program package VEC （Visual computing in Electron Crystallography） has been revised such that （i） a program converting one-line symbols to two-line symbols of （3＋1）-dimensional superspace groups has been incorporated into VEC so that the latter can interpret both kinds of symbols; （ii） a bug in calculating structure factors of onedimensionally incommensurate modulated crystals has been fixed. The correction has been verified by successfully matching the experimental electron microscopy image of an incommensurate crystal with a series of simulated images. The precompiled revised version of VEC and relevant materials are available on the Web at http：//cryst.iphy.ac.cn.

Presentation of the French Society of Mineralogyand Crystallography(SFMC)

The French Society of Mineralogy and Crystallography is honoured to be invited to give a short presentation of its activity to the Chinese Society for Mineralogy,Petrology and Geochemistry.BRIEF HISTORY AND SOME FRENCH FOUNDERS OF

Complex Formation of 1,6-Anhydro-<i>β</i>-Maltose and Sodium Ions Using Single-Crystal X-Ray Crystallography and NMR Spectroscopy

Complex formation of 1,6-anhydro-β-maltose and sodium ions was characterized using single-crystal X-ray crystallography and solution- and solid-state NMR spectroscopy. The 7-coordination structure, comprising two 1,6-anhydro-β-maltoses, a thiocyanate ion and a sodium ion, was identified in the crystal of the complex, where a sodium ion was positioned in the center of the pentagon. In the NMR study, the line broadening of 23Na signals and the decrease of the spin-lattice relaxation times (T1) of 23Na were observed in CD3OD in the presence of 1,6-anhydro-β-maltose, indicating complex formation.

Effect of Calcinations Temperature on Crystallography and Nanoparticles in ZnO Disk

We proposed a good calcinations condition of the ZnO disk to control the crystallography and nanoparticles in ZnO disk. The crystallography of precursor powder and disk powder were analyzed by the X-ray diffraction (XRD). The mean nanoparticles of ZnO disk was determinate by XRD results and observed by scanning electron microscope. The temperature ranges of 400℃ to 650℃ in air for 30 minutes were used calcinations ZnO disk. These temperature can be controlled the single phase, lattice parameters, unit cell volume, crystalline size, d-value, texture coefficient and bond lengths of Zn–Zn, Zn–O and O–O which correspond significantly the hexagonal crystal structure. The nanoparticles were small changed mean of 76.59 nm at the calcinations temperature range.

Determination of multilevel chirality in nickel molybdate films by electron crystallography

Chiral inorganic materials have attracted great attention owning to their unique physical and chemical properties attributed to the symmetry-breaking of their nanostructures.Chiral inorganic materials can be endowed with chiral geometric configurations from achiral space group crystals through lattice twisting,screw dislocations or hierarchical self-assembled spiral morphologies,showing various characteristic chiral anisotropy.However,the multilevel chirality in chiral nickel molybdate films(CNMFs)remains to be elaborately excavated.In this paper,we report three hierarchical levels of chirality in CNMFs,spanning from the atomic to the micron scale,including primary helically coiled nanoflakes with twisted atomic crystal lattices,secondary helical stacking of layered nanoflakes,and tertiary asymmetric morphology between adjacent nanoparticles.Our findings may enrich the chiral self-assembly structural types and provide valuable insights for the comprehensive analysis path of hierarchical chiral crystals.

FL-Online:An x-ray crystallographic web-server for atomic-scale structure analysis of biomolecule

FL-Online(http://fanlab.ac.cn) is an out-of-box modern web service featuring a user-friendly interface and simplified parameters, providing academic users with access to a series of online programs for biomolecular crystallography, including SAPI-online, OASIS-online, C-IPCAS-online and a series of upcoming software releases. Meanwhile, it is a highly scalable and maintainable web application framework that provides a powerful and flexible solution for academic web development needs. All the codes are open-source under MIT licenses in GitHub.

Pre-existing orthorhombic embryos-induced hexagonal-orthorhombic martensitic transformation in MnNiSi_(1-x)(CoNiGe)_x alloy

The thermal-elastic martensitic transformation from high-temperature Ni_(2)In-type hexagonal structure to low-temperature TiNiSi-type orthorhombic structure has been widely studied in MnMX(M=Ni or Co,and X=Ge or Si)alloys.However,the answer to how the orthorhombic martensite nucleates and grows within the hexagonal parent is still unclear.In this work,the hexagonal-orthorhombic martensitic transformation in a Co and Ge co-substituted MnNiSi is investigated.One can find some orthorhombic laths embedded in the hexagonal parent at a temperature above the martensitic transformation start temperature(M_(s)).With the the sample cooing to M_(s),the laths turn broader,indicating that the martensitic transformation starts from these pre-existing orthorhombic laths.Microstructure observation suggests that these pre-existing orthorhombic laths do not originate from the hexagonal-orthorhombic martensitic transformation because of the difference between atomic occupations of doping elements in the hexagonal parent and those in the preexisting orthorhombic laths.The phenomenological crystallographic theory and experimental investigations prove that the pre-existing orthorhombic lath and generated orthorhombic martensite have the same crystallography relationship to the hexagonal parent.Therefore,the orthorhombic martensite can take these pre-existing laths as embryos and grow up.This work implies that the martensitic transformation in MnNiSi_(1-x)(CoNiGe)_(x) alloy is initiated by orthorhombic embryos.

An introduction to computational crystallography:the relationship between aluminum-based spinel structures and their morphologies

The computational crystallography is proposed. Its basic concept and research method are systematically introduced, with aluminum-based spinel (ABS) as an example, through (i) selecting basic crystal structural unit, (ii) determining the mathematical expression of crystal structure, (iii) computing the stability energy of growth unit and finding out which is (are) favorable one(s), and (iv) describing the formation process of crystal morphology. The morphology of ABS deduced from the computation is in excellent agreement with that from hydrothermal experiments.

Combination of NMR spectroscopy and X-ray crystallography offers unique advantages for elucidation of the structural basis of protein complex assembly

NMR spectroscopy and X-ray crystallography are two premium methods for determining the atomic structures of macro-biomolecular complexes.Each method has unique strengths and weaknesses.While the two techniques are highly complementary,they have generally been used separately to address the structure and functions of biomolecular complexes.In this review,we emphasize that the combination of NMR spectroscopy and X-ray crystallography offers unique power for elucidating the structures of complicated protein assemblies.We demonstrate,using several recent examples from our own laboratory,that the exquisite sensitivity of NMR spectroscopy in detecting the conformational properties of individual atoms in proteins and their complexes,without any prior knowledge of conformation,is highly valuable for obtaining the high quality crystals necessary for structure determination by X-ray crystallography.Thus NMR spectroscopy,in addition to answering many unique structural biology questions that can be addressed specifically by that technique,can be exceedingly powerful in modern structural biology when combined with other techniques including X-ray crystallography and cryo-electron microscopy.

Microstructure evolution and crystallography of directionally solidified Al2O3/Y3Al5O12 eutectic ceramics prepared by the modified Bridgman method

Large size,high-density(99.97%)and well-organized Al2O3/Y3Al5O12(YAG)eutectic ceramics were prepared by the modified Bridgman method.The evolution of the three dimensional microstructure and micropores were investigated.The diameter of the micro-pores and the porosity decreased during directional solidification.The average equivalent diam eter of the micro-pores was 2.41μm in the well-prepared eutectic ceramics.Most of the pores(98.07%)were smaller than 4μm.These data are comparable to those prepared by the optical floating zone method.The as-grown eutectic ceramics were polycrystalline,but the interfaces were well-bonded and there were no amorphous phases in the microstructure.The misfits of the different crystallographic relationships were calculated,and the bottleneck of the single-crystal preparation was identified.These results could provide theoretical guidance for the preparation of large,single-crystal Al2O3/YAG eutectic ceramics by the modified Bridgman method.

Direct demodulation method for heavy atom position determination in protein crystallography

The first step of phasing in any de novo protein structure determination using isomorphous replacement （IR） or anomalous scattering （AD） experiments is to find heavy atom positions. Traditionally, heavy atom positions can be solved by inspecting the difference Patterson maps. Due to the weak signals in isomorphous or anomalous differences and the noisy background in the Patterson map, the search for heavy atoms may become difficult. Here, the direct demodulation （DD） method is applied to the difference Patterson maps to reduce the noisy backgrounds and sharpen the signal peaks. The real space Patterson search by using these optimized maps can locate the heavy atom positions more accurately. It is anticipated that the direct demodulation method can assist in heavy atom position determination and facilitate the de novo structure determination of proteins.

On intergranular mechanical interactions and the theory of deformation crystallography of metals

The equilibrium of intergranular stress and strain can be realized simultaneously,whereas five independent slip systems of the Taylor principle and the criterion of minimal internal work are unnecessary.In fact,the Taylor principle applied in current theories is incorrect both in practice and theory,in which the activation mechanism of plastic deformation systems must violate the Schmid’s law and deviate from the elastic-plastic characteristics of deformed matrix.The intergranular reaction stress(RS)during deformation can be calculated according to Hooke’s law and elastic limit without additional subjective presupposition,therefore the RS theory is established intuitively.Under the combination of the RS(the intergranular elastic effect)and the external loading the slips penetrating grains are activated and produce deformation texture,but certain non-penetrating slips near grain boundaries will become active(the intergranular plastic effect)and produce some random texture when a RS reaches the yield strength of grains.The RS theory is simple,intuitive and reasonable,based on which the texture simulation can well reproduce the texture formation of various metals under different external loadings and under different crystallographic mechanisms.

Crystallography of the martensitic transformation between Ni_2In-type hexagonal and TiNiSi-type orthorhombic phases

MnMX(M=Co or Ni,X=Si or Ge)alloys,experiencing structural transformation between Ni_(2) In-type hexagonal and TiNiSi-type orthorhombic phases,attract considerable attention due to their potential applications as room-temperature solid refrigerants.Although lots of studies have been carried out on how to tune this transformation and obtain large entropy change in a wide temperature region,the crystallography of this martensitic transformation is still unknown.The biggest obstacle for crystallography investigation is to obtain a bulk sample,in which hexagonal and orthorhombic phases coexist,because the MnMX alloys will fragment into powders after experiencing the transformation.For this reason,we carefully tune the transformation temperature to be slightly below 300 K.In that case,a bulk sample with small amounts of orthorhombic phases distributed in hexagonal matrix is obtained.Most importantly,there are no cracks between the two phases.It facilities us to investigate the microstructure using electron microscope.The obtained results indicate that the orientation relationship between hexagonal and orthorhombic structures is[4223]_(h)//[120]_(o)&(0110)_(h)//(001)_(o) and the habit plane is{2113.26}_(h).WLR theory is also adopted to calculate the habit plane.The calculated result agrees well with the measured one.Our work reveals the crystallography of hexagonal-orthorhombic transformation for the first time and is helpful for understanding the transformation-associated physical effects in MnMX alloys.