In-house high-energy-remote SAD phasing using the magic triangle: how to tackle the P1 low symmetry using multiple orientations of the same crystal of human IBA57 to increase the multiplicity

2019 ◽  
Vol 75 (3) ◽  
pp. 317-324 ◽  
Author(s):  
Spyridon Gourdoupis ◽  
Veronica Nasta ◽  
Simone Ciofi-Baffoni ◽  
Lucia Banci ◽  
Vito Calderone
Keyword(s):  
Data Processing ◽  
Model Building ◽  
Real Data ◽  
Threshold Value ◽  
High Energy ◽  
Software Developers ◽  
Data Set ◽  
Structure Solution ◽  
Sad Phasing ◽  
Low Symmetry

This article describes the approach used to solve the structure of human IBA57 in-house by 5-amino-2,4,6-triiodoisophthalic acid (I3C) high-energy-remote single-wavelength anomalous dispersion (SAD) phasing. Multiple orientations of the same triclinic crystal were exploited to acquire sufficient real data multiplicity for phasing. How the collection of an in-house native data set and its joint use with the I3C derivative through a SIRAS approach decreases the data multiplicity needed by almost 50% is described. Furthermore, it is illustrated that there is a clear data-multiplicity threshold value for success and failure in phasing, and how adding further data does not significantly affect substructure solution and model building. To our knowledge, this is the only structure present in the PDB that has been solved in-house by remote SAD phasing in space group P1 using only one crystal. All of the raw data used, derived from the different orientations, have been uploaded to Zenodo in order to enable software developers to improve methods for data processing and structure solution, and for educational purposes.

scholarly journals Optimization in S-SAD phasing - difference between solved and unsolved structure

2014 ◽  
Vol 70 (a1) ◽  
pp. C613-C613
Author(s):  
Jan Stránský ◽  
Tomáš Kovaľ ◽  
Lars Østergaard ◽  
Jarmila Dušková ◽  
Tereza Skálová ◽  
...  
Keyword(s):  
Data Processing ◽  
De Novo ◽  
Protein Structures ◽  
X Ray Diffraction ◽  
X Ray ◽  
Structure Solution ◽  
Sad Phasing ◽  
Optimal Values ◽  
Grant Agency ◽  
Intensity Reading

Development of X-ray diffraction technologies have made de novo phasing of protein structures by single-wavelength anomalous dispersion by sulphur (S-SAD) more common. As anomalous differences in the sulphur atomic factors are in the order of errors of measurement, careful intensity reading and data processing are crucial. S-SAD was used for de novo phasing of a small 12 kDa protein with 4 sulphur atoms per molecule at 2.3 Å, where the data did not enable a straightforward structure solution. Data processing was performed using XDS [1] and scaling using XSCALE. The sulphur substructure was determined by SHELXD [2] and phases were obtained from SHELXE [2]. Both algorithms strongly depend on input parameters and default values did not lead to the correct phases. Therefore a systematic search of optimal values of several parameters was used to find a solution. This method helped to confirm sulphur substructure and to differentiate the handedness of the solutions. Moreover, a script for comfortable conversion of SHELX outputs to MTZ format was developed, using programmes included in the CCP4 package [3]. The previously unsolvable protein structure was successfully resolved with the described procedure. This work was supported by the Grant Agency of the Czech Technical University in Prague, (SGS13/219/OHK4/3T/14), the Czech Science Foundation (P302/11/0855), project BIOCEV CZ.1.05/1.1.00/02.0109 from the ERDF.

scholarly journals Data processing pipeline for serial femtosecond crystallography at SACLA

2016 ◽  
Vol 49 (3) ◽  
pp. 1035-1041 ◽  
Author(s):  
Takanori Nakane ◽  
Yasumasa Joti ◽  
Kensuke Tono ◽  
Makina Yabashi ◽  
Eriko Nango ◽  
...  
Keyword(s):  
Data Processing ◽  
Data Acquisition ◽  
Real Time ◽  
Data Set ◽  
Hit Rate ◽  
Processing Pipeline ◽  
Structure Solution ◽  
Two Stages ◽  
Serial Femtosecond Crystallography ◽  
Detector Saturation

A data processing pipeline for serial femtosecond crystallography at SACLA was developed, based onCheetah[Bartyet al.(2014).J. Appl. Cryst.47, 1118–1131] andCrystFEL[Whiteet al.(2016).J. Appl. Cryst.49, 680–689]. The original programs were adapted for data acquisition through the SACLA API, thread and inter-node parallelization, and efficient image handling. The pipeline consists of two stages: The first, online stage can analyse all images in real time, with a latency of less than a few seconds, to provide feedback on hit rate and detector saturation. The second, offline stage converts hit images into HDF5 files and runsCrystFELfor indexing and integration. The size of the filtered compressed output is comparable to that of a synchrotron data set. The pipeline enables real-time feedback and rapid structure solution during beamtime.

scholarly journals Adventures in Phasing: Flavivirus NS1 solved by low resolution native S-SAD

2014 ◽  
Vol 70 (a1) ◽  
pp. C603-C603
Author(s):  
David Akey ◽  
William Brown ◽  
Jamie Konwerski ◽  
Craig Ogata ◽  
Richard Kuhn ◽  
...  
Keyword(s):  
Model Building ◽  
Genome Replication ◽  
Structural Protein ◽  
Low Resolution ◽  
West Nile Fever ◽  
Data Set ◽  
Phase Calculation ◽  
Poor Indicator ◽  
Final Data ◽  
Sad Phasing

We used native sulfur-SAD phasing to determine a novel structure of significant health importance, the flaviviruses non-structural protein 1 (NS1). Flaviviruses cause many diseases including dengue and West Nile fever. NS1 functions in both genome replication and immune system evasion. Full length, glycosylated NS1 was expressed in insect cells and crystallized. Due to difficulties with protein expression SeMet phasing was not practical, and we embarked on an effort to use sulfur-SAD phasing. To optimize the probability of observing the estimated 1.5% S-anomalous signal, we used inverse beam protocol at 7.1 keV with 50wedges and 0.50oscillations. Crystals typically diffracted to ~3.0 Å. Pairwise comparisons of anomalous correlation coefficient (AnomCC) and Rmerge in the highest intensity (low resolution) bins were used to decide which crystals to include in the final data set. Crystals which when compared to other crystals consistently had AnomCC < 0, or Rmerge > 7.5% in the low resolution bin were excluded. Data from 18 of 28 crystals were combined to generate a data set with ~100 fold anomalous multiplicity. The final data set was of high quality by I/σI and CC1/2 metrics with a positive AnomCC to ~5.4 Å. Sulfur sites were found with SHELXD using data to 5.2 Å. Phases calculated to 4.5 Å by SHELXE and extended to 3.0 Å with DM were of sufficient quality to autobuild ~75% of the final model. The NS1 structure was complete with the exception of one 20-residue internal loop, and glycosylation was observed at expected sites. Although Rmerge values were high for the combined data (30% overall, 9% low-res, 900% hi-res), model building and refinement proceeded smoothly, supporting the notion that Rmerge is a poor indicator of data quality for purposes of refinement and may also be a poor indicator for purposes of phasing. The effects of data multiplicity and resolution on S-site determination, phase calculation and phase extension were investigated.

scholarly journals Automatic wave-equation migration velocity analysis by focusing subsurface virtual sources

Geophysics ◽  
2018 ◽  
Vol 83 (2) ◽  
pp. U1-U8 ◽  
Author(s):  
Bingbing Sun ◽  
Tariq Alkhalifah
Keyword(s):  
Wave Equation ◽  
Model Building ◽  
Waveform Inversion ◽  
Synthetic Data ◽  
Real Data ◽  
Migration Velocity ◽  
Velocity Analysis ◽  
Data Set ◽  
Migration Velocity Analysis ◽  
Band Limited

Macro-velocity model building is important for subsequent prestack depth migration and full-waveform inversion. Wave-equation migration velocity analysis uses the band-limited waveform to invert for velocity. Normally, inversion would be implemented by focusing the subsurface offset common-image gathers. We reexamine this concept with a different perspective: In the subsurface offset domain, using extended Born modeling, the recorded data can be considered as invariant with respect to the perturbation of the position of the virtual sources and velocity at the same time. A linear system connecting the perturbation of the position of those virtual sources and velocity is derived and solved subsequently by the conjugate gradient method. In theory, the perturbation of the position of the virtual sources is given by the Rytov approximation. Thus, compared with the Born approximation, it relaxes the dependency on amplitude and makes the proposed method more applicable for real data. We determined the effectiveness of the approach by applying the proposed method on isotropic and anisotropic vertical transverse isotropic synthetic data. A real data set example verifies the robustness of the proposed method.

scholarly journals Pushing the limits of sulfur SAD phasing:de novostructure solution of the N-terminal domain of the ectodomain of HCV E1

2014 ◽  
Vol 70 (8) ◽  
pp. 2197-2203 ◽  
Author(s):  
Kamel El Omari ◽  
Oleg Iourin ◽  
Jan Kadlec ◽  
Richard Fearn ◽  
David R. Hall ◽  
...  
Keyword(s):  
Data Collection ◽  
Crystal Structures ◽  
Model Building ◽  
Heavy Atom ◽  
Data Set ◽  
X Ray ◽  
Terminal Domain ◽  
Structure Solution ◽  
Phase Extension ◽  
Resolution Model

Single-wavelength anomalous dispersion of S atoms (S-SAD) is an elegant phasing method to determine crystal structures that does not require heavy-atom incorporation or selenomethionine derivatization. Nevertheless, this technique has been limited by the paucity of the signal at the usual X-ray wavelengths, requiring very accurate measurement of the anomalous differences. Here, the data collection and structure solution of the N-terminal domain of the ectodomain of HCV E1 from crystals that diffracted very weakly is reported. By combining the data from 32 crystals, it was possible to solve the sulfur substructure and calculate initial maps at 7 Å resolution, and after density modication and phase extension using a higher resolution native data set to 3.5 Å resolution model building was achievable.

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

2011 ◽  
Vol 19 (1) ◽  
pp. 19-29 ◽  
Author(s):  
James Doutch ◽  
Michael A. Hough ◽  
S. Samar Hasnain ◽  
Richard W. Strange
Keyword(s):  
Model Building ◽  
De Novo ◽  
Protein Structures ◽  
Anomalous Scattering ◽  
X Ray ◽  
Long Wavelength ◽  
Structure Solution ◽  
Average Proportion ◽  
Sad Phasing

The sulfur SAD phasing method allows the determination of protein structuresde novowithout 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 trimericAchromobacter cycloclastesnitrite 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 forautomatedstructure 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) forAcNiR 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.

scholarly journals STEREOTOMOGRAPHY FOR VELOCITY MODEL ESTIMATION IN SEISMIC IMAGING: APPLICATION TO REAL DATA FROM JEQUITINHONHA SEDIMENTARY BASIN

2012 ◽  
Vol 30 (4) ◽  
pp. 473 ◽  
Author(s):  
Felipe A. Terra ◽  
Jessé C. Costa ◽  
Amin Bassrei
Keyword(s):  
Model Building ◽  
Seismic Imaging ◽  
Seismic Velocity ◽  
Synthetic Data ◽  
Structural Complexity ◽  
Real Data ◽  
Velocity Model ◽  
Common Source ◽  
Model Estimation ◽  
Data Set

O imageamento sísmico em profundidade é um desafio em áreas geologicamente complexas, onde a velocidade sísmica apresenta variação lateral. Porém, para se obter sucesso no imageamento sísmico em profundidade é necessário que se tenha uma estimativa confiável do modelo de velocidade. A estereotomografia é uma ferramenta efetiva para se alcançar esse propósito. Também denominada de tomografia de inclinação, ela utiliza as vagarosidades e os tempos de trânsito selecionados de famílias de fonte comum e de receptor comum. Nós avaliamos uma alternativa da estereotomografia para a construção do modelo de velocidades. O algoritmo foi validado no conjunto de dados sintéticos Marmousoft e também em dados reais provenientes da Bacia do Jequitinhonha, Brasil, numa região de talude continental. Este conjunto de dados com complexidade estrutural demandou um controle de alta qualidade na seleção de eventos, numa escolha criteriosa dos parâmetros de regularização, e a atenuação de múltiplas de superfície livre. Os resultados tanto para os dados sintéticos como para os reais mostraram a viabilidade computacional e precisão do método. ABSTRACT. Seismic imaging in depth is a challenge in geologically complex areas, where the seismic velocity varies laterally. The estimation of a reliable velocity model is necessary in order to succeed in seismic depth imaging. Stereotomography is an effective tool to achieve this purpose. Also called slope tomography, it uses the slowness and picked traveltimes from reflection events picked in common source and common receiver gathers. We evaluate an alternative implementation of stereotomography for velocity model building. The algorithm was validated in the Marmousoft synthetic data set and also used for velocity model estimation in acontinental slope region, using real data from Jequitinhonha Basin, Brazil. This data set of structural complexity demanded a high quality control of event selection forpicking, judicious choice of regularization parameters and free surface multiple attenuation. The results for both the synthetic and real data have shown the computational feasibility and accuracy of this method.Keywords: stereotomography, regularization, Jequitinhonha Basin

In situ irradiation effects studies in medium- and high-voltage TEM

1995 ◽  
Vol 53 ◽  
pp. 234-235
Author(s):  
Charles W. Allen
Keyword(s):  
Cross Section ◽  
Particle Flux ◽  
Threshold Value ◽  
High Energy ◽  
Irradiation Damage ◽  
Defect Complexes ◽  
Lattice Position ◽  
Electrons And Ions ◽  
The Masses

With respect to structural consequences within a material, energetic electrons, above a threshold value of energy characteristic of a particular material, produce vacancy-interstial pairs (Frenkel pairs) by displacement of individual atoms, as illustrated for several materials in Table 1. Ion projectiles produce cascades of Frenkel pairs. Such displacement cascades result from high energy primary knock-on atoms which produce many secondary defects. These defects rearrange to form a variety of defect complexes on the time scale of tens of picoseconds following the primary displacement. A convenient measure of the extent of irradiation damage, both for electrons and ions, is the number of displacements per atom (dpa). 1 dpa means, on average, each atom in the irradiated region of material has been displaced once from its original lattice position. Displacement rate (dpa/s) is proportional to particle flux (cm-2s-1), the proportionality factor being the “displacement cross-section” σD (cm2). The cross-section σD depends mainly on the masses of target and projectile and on the kinetic energy of the projectile particle.

EXPONENTIATED HALF-LOGISTIC LOMAX DISTRIBUTION WITH PROPERTIES AND APPLICATION

2019 ◽  
Vol XVI (2) ◽  
pp. 1-11
Author(s):  
Farrukh Jamal ◽  
Hesham Mohammed Reyad ◽  
Soha Othman Ahmed ◽  
Muhammad Akbar Ali Shah ◽  
Emrah Altun
Keyword(s):  
Real Data ◽  
Continuous Model ◽  
Model Parameters ◽  
Data Set ◽  
Lomax Distribution ◽  
Mathematical Properties ◽  
Proposed Model ◽  
Probability Weighted Moment ◽  
Record Statistics ◽  
Maximum Likelihood Criterion

A new three-parameter continuous model called the exponentiated half-logistic Lomax distribution is introduced in this paper. Basic mathematical properties for the proposed model were investigated which include raw and incomplete moments, skewness, kurtosis, generating functions, Rényi entropy, Lorenz, Bonferroni and Zenga curves, probability weighted moment, stress strength model, order statistics, and record statistics. The model parameters were estimated by using the maximum likelihood criterion and the behaviours of these estimates were examined by conducting a simulation study. The applicability of the new model is illustrated by applying it on a real data set.

Evaluation for estimating of the PDF and the CDF of Generalized Inverted Exponential Distribution with Application in Industry

2020 ◽  
pp. 507-522
Author(s):  
Parisa Torkaman
Keyword(s):  
Least Squares ◽  
Exponential Distribution ◽  
Mean Squared Error ◽  
Weighted Least Squares ◽  
Real Data ◽  
Minimum Variance ◽  
Cumulative Distribution ◽  
Estimation Methods ◽  
Data Set ◽  
Better Than

The generalized inverted exponential distribution is introduced as a lifetime model with good statistical properties. This paper, the estimation of the probability density function and the cumulative distribution function of with five different estimation methods: uniformly minimum variance unbiased(UMVU), maximum likelihood(ML), least squares(LS), weighted least squares (WLS) and percentile(PC) estimators are considered. The performance of these estimation procedures, based on the mean squared error (MSE) by numerical simulations are compared. Simulation studies express that the UMVU estimator performs better than others and when the sample size is large enough the ML and UMVU estimators are almost equivalent and efficient than LS, WLS and PC. Finally, the result using a real data set are analyzed.

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