SAD phasing by OASIS at different resolutions down to 0.30 nm and below

Single-wavelength anomalous diffraction （SAD） phasing is increasingly important in solving de novo protein structures. Direct methods have been proved very efficient in SAD phasing. This paper aims at probing the low-resolution limit of direct-method SAD phasing. Two known proteins TT0570 and Tom70p were used as test samples. Sulfur-SAD data of the protein TT0570 were collected with conventional Cu-Kα source at 0.18 nm resolution. Its truncated subsets respectively at 0.21, 0.30, 0.35 and 0.40 nm resolutions were used in the test. TT0570 Cu-Kα sulfur-SAD data have an expected Bijvoet ratio 〈 ｜△F｜ 〉 / 〈 F 〉 ～ 0.55%. In the 0.21 nm case, a single run of OASIS-DM-ARP/wARP led automatically to a model containing 1178 of the total 1206 residues all docked into the sequence. In 0.30 and 0.35 nm cases, SAD phasing by OASIS-DM led to traceable electron density maps. In the 0.40 nm case, SAD phasing by OASIS-DM resulted in a degraded electron density map, which may be difficult to trace but still contains useful secondary-structure information. Test on real 0.33 nm selenium-SAD data of the protein Tom70p showed that even automatic model building was not successful, the combination of manual tracing and direct-method fragment extension was capable of significantly improving the electron-density map. This provides the possibility of effectively improving the manually built model before structure refinement is performed.     

Combining SAD/SIR iteration and MR iteration in partial-model extension of proteins

There are two kinds of dual-space partial-model extensions which involve the direct-method program OASIS. The first kind, named SAD/SIR iteration, uses SAD/SIR information, while the second kind, named molecular replacement (MR) iteration, does not use that information. In general, the SAD/SIR iteration is more powerful since more experimental information is used. However, in most cases when protein structures are solved with the molecular replacement method, SAD/SIR information is not available. Thus the MR iteration is particularly useful for the completion of models from molecular replacement. The SAD/SIR iteration will be automatically used in OASIS for data sets containing SAD/SIR signals, while the MR iteration will be dedicated to data sets without SAD/SIR signals. The present paper shows that for data containing SAD/SIR signals, a combination of SAD/SIR iteration and MR iteration could lead to significantly better results than that obtained from the SAD/SIR iteration alone.     

Use of iterative OASIS with low resolution SAD laboratory X-ray source (Cr Kα) data sets

Anomalous scattering methods are widely used for phasing macromolecular structures. OASIS program works on a direct methods procedure and is used to break the phase ambiguity intrinsic in a single wavelength anomalous diffraction (SAD) experiment. An iterative phasing/model-building procedure for processing SAD data includes the initial direct method phasing of SAD data, density modification, automatic model building and direct methods phasing of SAD data with feed back from partial structure information. This dual-space procedure has been tested on two experimental Cr Kα SAD data sets, 2.3 ? for S-SAD and 2.4 ? for I-SAD, of an enzyme glucose isomerase with an approximate molecular weight of 44 kDa (388 residues). HYSS in PHENIX was used to locate the anomalous scatterers for both the data sets (11 sulfurs for 2.3 ? data and 9 iodines for 2.4 ? data). Phasing and density modification were carried out using OASIS, DM and model building was then carried out using ARP/wARP. Two iterative cycles were necessary for the successful structure solution and refinement of the 2.3 ? data set which built 384 residues out of 388. Regular ARP/wARP failed for the 2.4 ? resolution data and hence the modified version of REFMAC5 was used in ARP/wARP. A successful model could be built after three iterative cycles of OASIS using this modified version which built 382 residues out of 388 residues. Minimal manual model building was required at this stage and the structure determination was completed using regular REFMAC5. All the computations mentioned here were carried out using Pentium IV PC.     

Challenges of sulfur SAD phasing as a routine method in macromolecular crystallography

The sulfur SAD phasing method allows the determination of protein structures de novo without reference to derivatives such as Se‐methionine. The feasibility for routine automated sulfur SAD phasing using a number of current protein crystallography beamlines at several synchrotrons was examined using crystals of trimeric Achromobacter cycloclastes nitrite reductase (AcNiR), which contains a near average proportion of sulfur‐containing residues and two Cu atoms per subunit. Experiments using X‐ray wavelengths in the range 1.9–2.4 Å show that we are not yet at the level where sulfur SAD is routinely successful for automated structure solution and model building using existing beamlines and current software tools. On the other hand, experiments using the shortest X‐ray wavelengths available on existing beamlines could be routinely exploited to solve and produce unbiased structural models using the similarly weak anomalous scattering signals from the intrinsic metal atoms in proteins. The comparison of long‐wavelength phasing (the Bijvoet ratio for nine S atoms and two Cu atoms is ～1.25% at ～2 Å) and copper phasing (the Bijvoet ratio for two Cu atoms is 0.81% at ～0.75 Å) for AcNiR suggests that lower data multiplicity than is currently required for success should in general be possible for sulfur phasing if appropriate improvements to beamlines and data collection strategies can be implemented.     

SIR phasing by combination of SOLVE/RESOLVE and dual-space fragment extension involving OASIS

A new phasing procedure has been proposed for dealing with single isomorphous replacement (SIR) x-ray diffraction data. The procedure combines {SOLVE/RESOLVE} with the dual-space fragment extension involving {OASIS}. Two sets of SIR data at 0.28~nm resolution taken from the protein (R)-phycoerythrin (PDB code: 1LIA) were used in the test. For one of the two SIR data sets, a default run of {SOLVE/RESOLVE} based on the heavy-atom substructure found by {SHLEXD} led automatically to an interpretable electron density map. {OASIS} could not effectively improve the result. For the other set of SIR data, {SOLVE/RESOLVE} resulted in a fragmented model consisting of 454 of the total 668 residues, in which only 29 residues were docked into the sequence. Based on this model, 7 iteration cycles of {OASIS-DM-RESOLVE} (build only) yielded automatically a model of 547 residues with 133 residues docked into the sequence. The overall-averaged phase error decreased considerably and the quality of electron density map was improved significantly. Two more cycles of iterative {OASIS}-{DM}-{RESOLVE} were carried out, in which the output phases and figures of merit from {DM} were merged with that from the original run of {SOLVE/RESOLVE} before they were passed onto {RESOLVE} (build only). This led automatically to a model containing 452 residues with 173 docked into the sequence. The resultant electron density map is manually traceable. It is concluded that when results of {SOLVE/RESOLVE} are not sufficiently satisfactory, the combination of {SOLVE/RESOLVE} and {OASIS}-{DM}-{RESOLVE} (build only) may significantly improve them.     

A comparison of SAD and two‐wavelength MAD phasing for radiation‐damaged Se‐MET crystals

Although a case has been made that single‐wavelength anomalous dispersion (SAD) is the optimal strategy for data collection in the presence of radiation damage, two‐wavelength MAD experiments at the inflection and a high‐energy remote point of the absorption edge have been shown to be a potentially successful alternative method. In order to further investigate the performance of both data collection strategies, a comparison of SAD and MAD phasing was carried out for increasingly damaged data sets from three different seleno‐methionine protein samples collected under similar experimental conditions. In all but one example the MAD phases appeared to be less affected than SAD phases with increasing exposure to X‐rays, and had a better overall success rate, indicating that this method should be given serious consideration when dealing with radiation‐sensitive crystals. Simultaneous data collection in wedges at all wavelengths seems to be a very important factor in the success of MAD experiments; the decreased absorbed dose resulting from eschewing data collection at the maximum f ′′ wavelength may play a less important role. Specific radiation damage to the selenium atoms is found to be a minor effect compared with the effect on the anomalous dispersion signal, although potentially large enough to be a useful contribution to phasing in both SAD and MAD experiments.     

OASIS4.0—a new version of the program OASIS for phasing protein diffraction data

<正>The program OASIS4.0 has been released.Apart from the improved single-wavelength anomalous diffraction (SAD) phasing algorithm described in a separate paper,an important new feature in this version is the automation of the iterative phasing and model-building process in solving protein structures.A new graphical user's interface(GUI) is provided for controlling and real-time monitoring the dual-space iterative process.The GUI is discussed in detail in the present paper.     

Reconstruction of $$ \tilde \tau _1 $$ mass at the LHC

The cascade mass reconstruction approach was used for mass reconstruction of the lightest $ \tilde \tau $ \tilde \tau produced at the LHC in the cascade decay $ \tilde g \to \tilde bb \to \tilde \chi _2^0 bb \to \tilde \tau _1 \tau bb \to \tilde \chi _1^0 \tau \tau bb $ \tilde g \to \tilde bb \to \tilde \chi _2^0 bb \to \tilde \tau _1 \tau bb \to \tilde \chi _1^0 \tau \tau bb . The $ \tilde \tau _1 $ \tilde \tau _1 mass was reconstructed assuming that masses of gluino, bottom squark, and two lightest neutralinos were reconstructed in advance. SUSY data sample sets for the SU(3) model point containing 160k events each were generated which corresponded to an integrated luminosity of about 8 fb⁻¹ at 14 TeV. These events were passed through the AcerDET detector simulator, which parametrized the response of a generic LHC detector. The mass of the $ \tilde \tau _1 $ \tilde \tau _1 was reconstructed with a precision of about 20% on average.     

Anomalous structure of the crust and mantle of mars

This study determined the contribution of Martian topography and the density jump at the Mohorovicic discontinuity (M) to the gravity in a quadratic approximation. It also resolved the problem of determining the possible depths of compensation for topography harmonics of various degrees and orders. It shows that all the topography compensation is within the depth range from 0 to 1400 km. Different topographic irregularities are most likely to be compensated at depths that correspond to the upper crust ($ \bar d = 4.5 \pm 3.7{\text{ km}} $ \bar d = 4.5 \pm 3.7{\text{ km}} ), crust-mantle transition layer ($ \bar d = 78 \pm 24{\text{ km}} $ \bar d = 78 \pm 24{\text{ km}} ), lithospheric boundary ($ \bar d = 200 \pm 34{\text{ km}} $ \bar d = 200 \pm 34{\text{ km}} ), upper-middle mantle transition layer ($ \bar d = 400 \pm 70{\text{ km}} $ \bar d = 400 \pm 70{\text{ km}} ), or middle-lower mantle transition layer ($ \bar d = 1120 \pm 180{\text{ km}} $ \bar d = 1120 \pm 180{\text{ km}} ). This paper presents the lateral distributions of compensation masses for these depths and the respective maps. According to calculations, stresses in the Martian crust and mantle may be as high as 10⁸ Pa. This paper shows that the topographic anomalies of the Tharsis volcanic plateau and the symmetric formation in the eastern hemisphere could have originated and be dynamically maintained by two plumes of melted mantle substance enriched with fluids; these plumes may have their origin at the boundary of the lower mantle.     

Backward pion-nucleon scattering

A global analysis of the world data on differential cross-sections and polarization asymmetries of backward pion-nucleon scattering for invariant collision energies above 3GeV is performed in a Regge model. Including the N_a\ensuremath N_{\alpha} , N_g\ensuremath N_{\gamma} , D_d\ensuremath \Delta_{\delta} and D_b\ensuremath \Delta_{\beta} trajectories, we reproduce both angular distributions and polarization data for small values of the Mandelstam variable u , in contrast to previous analyses. The model amplitude is used to obtain evidence for baryon resonances with mass below 3GeV. Our analysis suggests a G₃₉\ensuremath G_{39} -resonance with a mass of 2.83GeV as member of the D_b\ensuremath \Delta_{\beta} -trajectory from the corresponding Chew-Frautschi plot.     

Production of strange secondaries in high-energy Σ<Superscript>−</Superscript><Emphasis Type="Italic">A</Emphasis> collisions

The WA89 Collaboration experimental data on production of Λ, Σ⁻, Σ⁺, Ξ⁻, Ω⁻ baryons, $ \bar \Lambda $ \bar \Lambda and $ \bar \Xi ^ + $ \bar \Xi ^ + antibaryons in Σ⁻ collisions with C and Cu targets at 345 GeV/c ($ \sqrt {s_{\Sigma N} } $ \sqrt {s_{\Sigma N} } ≈ 25.5 GeV) in the frame of the Quark-Gluon String Model is described. The comparison of the theoretical results with the experimental data is discussed. Finally, some relations among the values of the model parameters obtained with the help of quark combinatorics are presented.     

Nuclear matrix elements for the resonant neutrinoless double electron capture

The rate of the neutrinoless double electron capture ( 0n\ensuremath 0\nu ECEC) decay with a resonance condition depends sensitively on the mass difference between the initial and final nuclei of decay. This is where the JYFLTRAP Penning-trap measurements at the JYFL become invaluable in estimation of the half-lives of these decays. In this work the resonant 0n\ensuremath 0\nu ECEC decay is discussed from the point of view of its theoretical aspects, in particular regarding the resonance condition and the involved nuclear matrix elements (NME). The associated decay amplitudes are derived and the calculations of the NMEs by the microscopic many-body approach of the multiple-commutator model are outlined. The resonant 0n\ensuremath 0\nu ECEC decays of ⁷⁴Ge\ensuremath {\rm ^{74}Ge} and ¹³⁶Ce\ensuremath {\rm ^{136}Ce} are discussed as applications of the theory framework.     

Abelian Sandpiles and the Harmonic Model

We present a construction of an entropy-preserving equivariant surjective map from the d-dimensional critical sandpile model to a certain closed, shift-invariant subgroup of \mathbbT^\mathbbZd{\mathbb{T}^{\mathbb{Z}^d}} (the ‘harmonic model’). A similar map is constructed for the dissipative abelian sandpile model and is used to prove uniqueness and the Bernoulli property of the measure of maximal entropy for that model.     

Electrical conductivity of a two-dimensional model for a structurally anisotropic composite

The electrical conductivity of a two-dimensional structurally anisotropic model for a composite is considered. The model represents an isotropic matrix with a system of nonconducting inclusions in the form of infinitely thin straight line segments (scratches). The scratches make an angle θ or −θ with a preferred axis (for definiteness, axis y) at the same probability, and their centers are chaotically distributed. An approximate effective medium method is used to obtain a general expression for the effective conductivity tensor $ \hat \sigma _e $ \hat \sigma _e of this model that is valid over a wide concentration range. In this approximation, both components of tensor are $ \hat \sigma _e $ \hat \sigma _e shown to vanish at the same percolation threshold, which is expressed explicitly. The conductivity of the model in a critical region is considered in terms of the similarity hypothesis.     

Absorption optique du compose mixte Ga1-xAlxSb,pres du bord d'absorption

The absorption coefficient and the photovoltage of the mixed compound Ga_(1-x)Al_xSb have been measured near the absorption edge, from single crystalline layers (x = 0.30, 0.34, 0.37, 0.40, 0.56). It has been estimated that the change of nature in optical transitions occurs for x included between 0.35 and 0.40.     

Neutral meson oscillations and equivalence principle for particles and antiparticles

Oscillations of neutral meson (K ⁰-$ \overline {K^0 } $ \overline {K^0 } , D ⁰-$ \overline {D^0 } $ \overline {D^0 } , and B ⁰-$ \overline {B^0 } $ \overline {B^0 } are extremely sensitive to the meson and antimeson energies at rest. This energy is determined as mc ²—with the corresponding inertial mass—and as the energy of gravitational interaction. Assuming that the CPT theorem is correct for inertial masses and estimating the gravitational potential for which the largest contribution originates from the field of the galaxy center, we obtain the estimate from experimental data on K ⁰-$ \overline {K^0 } $ \overline {K^0 } oscillations:

Constraints on the generalized natural inflation after Planck 2018

Based on the dynamics of single scalar field slow-roll inflation and the theory of reheating, we investigate the generalized natural inflationary (GNI) model. We introduce constraints on the scalar spectral index \begin{document}$n_{s}$\end{document} and the tensor-to scalar ratio r for the \begin{document}$\Lambda$\end{document}CDM \begin{document}$+r$\end{document} model, according to the latest data from Planck 2018 TT, TE, EE+low E+lensing (P18) and BICEP2/Keck 2015 season (BK15), i.e., with \begin{document}$n_{s}=0.9659\pm0.0044$\end{document} at 68% confidence level (CL), and \begin{document}$r<0.0623$\end{document} at 95% CL. We find that the GNI model is favored by P18 and BK15 in the ranges \begin{document}$\log_{10}(f/M_{p})= 0.62^{+0.17}_{-0.18}$\end{document} and \begin{document}$m=0.35^{+0.13}_{-0.23}$\end{document} at 68% CL. In addition, the corresponding predictions of generalized and two-phase reheating are discussed. It follows that the parameter m has significant effect on the model behavior.     

Spin correlations in the ΛΛ and Λ$$ \bar \Lambda $$ systems generated in relativistic heavy-ion collisions

Spin correlations for the ΛΛ and Λ$ \bar \Lambda $ \bar \Lambda pairs, generated in relativistic heavy-ion collisions, and related angular correlations at the joint registration of hadronic decays of two hyperons, in which space parity is not conserved, are analyzed. The correlation tensor components can be derived from the double angular distribution of products of two decays by the method of “moments”. The properties of the “trace” of the correlation tensor (a sum of three diagonal components), determining the relative fractions of the triplet states and singlet state of respective pairs, are discussed. Spin correlations for two identical particles (ΛΛ) and two nonidentical particles (Λ$ \bar \Lambda $ \bar \Lambda ) are considered from the viewpoint of the conventional model of one-particle sources. In the framework of this model, correlations vanish at sufficiently large relative momenta. However, under these conditions, in the case of two nonidentical particles (Λ$ \bar \Lambda $ \bar \Lambda ) a noticeable role is played by two-particle annihilation (two-quark, two-gluon) sources, which lead to the difference of the correlation tensor from zero. In particular, such a situation may arise when the system passes through the “mixed phase.”     

Low-regularity Schrödinger maps,II: global well-posedness in dimensions <Emphasis Type="Italic">d</Emphasis> ≥ 3

In dimensions d ≥ 3, we prove that the Schrödinger map initial-value problem

$ \left\{ \begin{array}{l} \partial_ts=s\times\Delta_x s\hbox{ on }\mathbb{R}^d\times\mathbb{R};\\ s(0)=s_0 \end{array} \right. $

is globally well-posed for small data s ₀ in the critical Besov spaces \({\dot{B}_Q^{d/2}(\mathbb{R}^d;\mathbb{S}^2)}\), \({Q\in\mathbb{S}^2}\).

     

Phasing of lysozyme using one－wavelength anomalous scattering of sulphur atoms through the combination of direct methods and density modification

A new method of combining one-wavelength anomalous scattering (OAS) phasing and density modification has been described, in which the improved phases from density modification axe re-introduced into OAS phasing. In this way, the phases could be improved iteratively until convergence. The OAS phasing method is based on the previously established sign-probability formula, which breaks the phase ambiguity in the OAS phasing. The implementation of this method has been available in CCP4 as OASIS. This method, although based on direct-methods, could also incorporate known phases and figures of merit into its sign-probability formula. In the implementation of OASIS, the known phases axe from the positions of the anomalous scatters. In the current method, the known phases are from the density modification. The current method was tested on phasing a lysozyme crystal using anomalous scattering of sulphur atoms with diffraction data collected on an in-house x-ray source. The resulting map was well connected for the backbone atoms and clearly traceable, with an average map correlation coefficient of 0.6622 for the backbone atoms.