New tools for serial crystallography: SPIND (sparse pattern auto-indexing) and DatView (exploring and optimizing large multi-crystal data sets)

KAMO and Blend provide particularly effective tools to automatically manage the merging of large numbers of data sets from serial crystallography. The requirement for manual intervention in the process can be reduced by extending Blend to support additional clustering options to increase the sensitivity to differences in unit cell parameters and to allow for clustering of nearly complete datasets on the basis of intensity or amplitude differences. If datasets are already sufficiently complete to permit it, apply KAMO once, just for reflections. If starting from incomplete datasets, one applies KAMO twice, first using cell parameters. In this step either the simple cell vector distance of the original Blend is used, or the more sensitive NCDist, to find clusters to merge to achieve sufficient completeness to allow intensities or amplitudes to be compared. One then uses KAMO again using the correlation between the reflections at the common HKLs to merge clusters in a way sensitive to structural differences that may not perturb the cell parameters sufficiently to make meaningful clusters.Many groups have developed effective clustering algorithms that use a measurable physical parameter from each diffraction still or wedge to cluster the data into categories which can then be merged to, hopefully, yield the electron density from a single protein iso-form. What is striking about many of these physical parameters is that they are largely independent from one another. Consequently, it should be possible to greatly improve the efficacy of data clustering software by using a multi-stage partitioning strategy. Here, we have demonstrated one possible approach to multi-stage data clustering. Our strategy was to use unit-cell clustering until merged data was of sufficient completeness to then use intensity based clustering. We have demonstrated that, using this strategy, we were able to accurately cluster data sets from crystals that had subtle differences.

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Data reduction for serial crystallography using a robust peak finder

Journal of Applied Crystallography ◽

10.1107/s1600576721007317 ◽

2021 ◽

Vol 54 (5) ◽

Author(s):

Marjan Hadian-Jazi ◽

Alireza Sadri ◽

Anton Barty ◽

Oleksandr Yefanov ◽

Marina Galchenkova ◽

...

Keyword(s):

Robust Statistics ◽

Probability Distributions ◽

Data Sets ◽

Time Data ◽

Peak Finding ◽

Short Period ◽

Serial Crystallography ◽

Diffraction Patterns ◽

Analyse Data ◽

Real Time Data Processing

A peak-finding algorithm for serial crystallography (SX) data analysis based on the principle of `robust statistics' has been developed. Methods which are statistically robust are generally more insensitive to any departures from model assumptions and are particularly effective when analysing mixtures of probability distributions. For example, these methods enable the discretization of data into a group comprising inliers (i.e. the background noise) and another group comprising outliers (i.e. Bragg peaks). Our robust statistics algorithm has two key advantages, which are demonstrated through testing using multiple SX data sets. First, it is relatively insensitive to the exact value of the input parameters and hence requires minimal optimization. This is critical for the algorithm to be able to run unsupervised, allowing for automated selection or `vetoing' of SX diffraction data. Secondly, the processing of individual diffraction patterns can be easily parallelized. This means that it can analyse data from multiple detector modules simultaneously, making it ideally suited to real-time data processing. These characteristics mean that the robust peak finder (RPF) algorithm will be particularly beneficial for the new class of MHz X-ray free-electron laser sources, which generate large amounts of data in a short period of time.

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Application and comparison of different tests on twinning by merohedry

Acta Crystallographica Section B Structural Science ◽

10.1107/s010876819900590x ◽

1999 ◽

Vol 55 (5) ◽

pp. 745-751 ◽

Cited By ~ 10

Author(s):

V. Kahlenberg

Keyword(s):

Single Crystal ◽

Crystal Structures ◽

Structure Analysis ◽

Structure Determination ◽

Data Sets ◽

Crystal Data ◽

Test Procedures ◽

Preliminary Stage ◽

Volume Fractions ◽

Inorganic Crystal

Three different tests on twinning by merohedry from the literature have been applied to single-crystal data sets of five different inorganic crystal structures. Although the three test procedures differ significantly with regard to their efficiency, in both detecting the existence of twinning and estimating the volume fractions of the twin individuals, they represent useful tools in the early stages of a structure analysis and should be applied routinely in the preliminary stage of a structure determination whenever a twinning by merohedry is possible.

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Merging of synchrotron serial crystallographic data by a genetic algorithm

Acta Crystallographica Section D Structural Biology ◽

10.1107/s2059798316012079 ◽

2016 ◽

Vol 72 (9) ◽

pp. 1026-1035 ◽

Cited By ~ 19

Author(s):

Ulrich Zander ◽

Michele Cianci ◽

Nicolas Foos ◽

Catarina S. Silva ◽

Luca Mazzei ◽

...

Keyword(s):

Genetic Algorithm ◽

Incomplete Data ◽

Catalytic Reactions ◽

Data Sets ◽

Data Set ◽

Small Oscillations ◽

New Methods ◽

Dynamic Events ◽

Serial Crystallography

Recent advances in macromolecular crystallography have made it practical to rapidly collect hundreds of sub-data sets consisting of small oscillations of incomplete data. This approach, generally referred to as serial crystallography, has many uses, including an increased effective dose per data set, the collection of data from crystals without harvesting (in situdata collection) and studies of dynamic events such as catalytic reactions. However, selecting which data sets from this type of experiment should be merged can be challenging and new methods are required. Here, it is shown that a genetic algorithm can be used for this purpose, and five case studies are presented in which the merging statistics are significantly improved compared with conventional merging of all data.

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Combined neutron powder and X-ray single-crystal diffraction refinement of the atomic structure and hydrogen bonding of goslarite (ZnSO4·7H2O)

Mineralogical Magazine ◽

10.1180/0026461056930249 ◽

2005 ◽

Vol 69 (3) ◽

pp. 259-271 ◽

Cited By ~ 10

Author(s):

J. L. Anderson ◽

R. C. Peterson ◽

I. P. Swainson

Keyword(s):

Hydrogen Bonding ◽

Single Crystal ◽

Atomic Structure ◽

Data Sets ◽

Crystal Data ◽

Single Crystal Diffraction ◽

Future Studies ◽

X Ray ◽

Hydration And Dehydration ◽

Phase Relationships

AbstractThe atomic structure of synthetic, deuterated goslarite (ZnSO4·7D2O), a = 11.8176(6) Å, b = 12.0755(7) Å, c = 6.8270(4)Å, space group P212121, Z = 4, has been refined in a combined neutron powder diffraction and X-ray single-crystal data refinement to wRp 1.92%, Rp 1.45% and R(F2) 12.66% for the neutron powder data contribution and R(F2) 8.72% for the X-ray single-crystal data contribution. Both data sets were necessary to achieve the best overall fit agreement in the Rietveld refinement and reasonable geometry within structural units. The results of this study confirm that the H-bonding scheme for goslarite is the same as that of the other epsomite group minerals. Small but significant variations of the Zn–O bond lengths can be attributed to details of the H bonds to the O atoms of the Zn octahedra. This investigation of the atomic structure and hydrogen bonding of goslarite is groundwork for future studies into phase relationships and the mechanisms of hydration and dehydration in the ZnSO4–H2O system.

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X-ray and UV radiation-damage-induced phasing using synchrotron serial crystallography

Acta Crystallographica Section D Structural Biology ◽

10.1107/s2059798318001535 ◽

2018 ◽

Vol 74 (4) ◽

pp. 366-378 ◽

Cited By ~ 5

Author(s):

Nicolas Foos ◽

Carolin Seuring ◽

Robin Schubert ◽

Anja Burkhardt ◽

Olof Svensson ◽

...

Keyword(s):

Success Rate ◽

Radiation Damage ◽

Uv Radiation ◽

De Novo ◽

Data Sets ◽

Individual Data ◽

High Quality ◽

X Ray ◽

Serial Crystallography

Specific radiation damage can be used to determine phasesde novofrom macromolecular crystals. This method is known as radiation-damage-induced phasing (RIP). One limitation of the method is that the dose of individual data sets must be minimized, which in turn leads to data sets with low multiplicity. A solution to this problem is to use data from multiple crystals. However, the resulting signal can be degraded by a lack of isomorphism between crystals. Here, it is shown that serial synchrotron crystallography in combination with selective merging of data sets can be used to determine high-quality phases for insulin and thaumatin, and that the increased multiplicity can greatly enhance the success rate of the experiment.

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Single-crystal diffraction at the Extreme Conditions beamline P02.2: procedure for collecting and analyzing high-pressure single-crystal data

Journal of Synchrotron Radiation ◽

10.1107/s0909049513018621 ◽

2013 ◽

Vol 20 (5) ◽

pp. 711-720 ◽

Cited By ~ 42

Author(s):

André Rothkirch ◽

G. Diego Gatta ◽

Mathias Meyer ◽

Sébastien Merkel ◽

Marco Merlini ◽

...

Keyword(s):

High Pressure ◽

Single Crystal ◽

Structure Refinement ◽

Extreme Conditions ◽

Data Sets ◽

Crystal Data ◽

Area Detector ◽

Data Formats ◽

Commercial Software Package ◽

Data Collections

Fast detectors employed at third-generation synchrotrons have reduced collection times significantly and require the optimization of commercial as well as customized software packages for data reduction and analysis. In this paper a procedure to collect, process and analyze single-crystal data sets collected at high pressure at the Extreme Conditions beamline (P02.2) at PETRA III, DESY, is presented. A new data image format called `Esperanto' is introduced that is supported by the commercial software packageCrysAlisPro(Agilent Technologies UK Ltd). The new format acts as a vehicle to transform the most common area-detector data formatsviaa translator software. Such a conversion tool has been developed and converts tiff data collected on a Perkin Elmer detector, as well as data collected on a MAR345/555, to be imported into theCrysAlisProsoftware. In order to demonstrate the validity of the new approach, a complete structure refinement of boron-mullite (Al5BO9) collected at a pressure of 19.4 (2) GPa is presented. Details pertaining to the data collections and refinements of B-mullite are presented.

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Solvent minimization induces preferential orientation and crystal clustering in serial micro-crystallography on micro-meshes,in situplates and on a movable crystal conveyor belt

Journal of Synchrotron Radiation ◽

10.1107/s1600577514017731 ◽

2014 ◽

Vol 21 (6) ◽

pp. 1231-1239 ◽

Cited By ~ 7

Author(s):

Alexei S. Soares ◽

Jeffrey D. Mullen ◽

Ruchi M. Parekh ◽

Grace S. McCarthy ◽

Christian G. Roessler ◽

...

Keyword(s):

Data Collection ◽

Conveyor Belt ◽

Preferential Orientation ◽

Quality Data ◽

Data Sets ◽

X Ray ◽

Replacement Solution ◽

Serial Crystallography ◽

Diffraction Patterns ◽

Lysozyme Crystals

X-ray diffraction data were obtained at the National Synchrotron Light Source from insulin and lysozyme crystals that were densely deposited on three types of surfaces suitable for serial micro-crystallography: MiTeGen MicroMeshes™, Greiner Bio-One Ltdin situmicro-plates, and a moving kapton crystal conveyor belt that is used to deliver crystals directly into the X-ray beam. 6° wedges of data were taken from ∼100 crystals mounted on each material, and these individual data sets were merged to form nine complete data sets (six from insulin crystals and three from lysozyme crystals). Insulin crystals have a parallelepiped habit with an extended flat face that preferentially aligned with the mounting surfaces, impacting the data collection strategy and the design of the serial crystallography apparatus. Lysozyme crystals had a cuboidal habit and showed no preferential orientation. Preferential orientation occluded regions of reciprocal space when the X-ray beam was incident normal to the data-collection medium surface, requiring a second pass of data collection with the apparatus inclined away from the orthogonal. In addition, crystals measuring less than 20 µm were observed to clump together into clusters of crystals. Clustering required that the X-ray beam be adjusted to match the crystal size to prevent overlapping diffraction patterns. No additional problems were encountered with the serial crystallography strategy of combining small randomly oriented wedges of data from a large number of specimens. High-quality data able to support a realistic molecular replacement solution were readily obtained from both crystal types using all three serial crystallography strategies.

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A tribenzylidenemethane–tantalum compound: some experiences with `inversion twinning'

Acta Crystallographica Section B Structural Science ◽

10.1107/s0108768195013255 ◽

1996 ◽

Vol 52 (3) ◽

pp. 465-470 ◽

Cited By ~ 3

Author(s):

W. P. Schaefer ◽

R. E. Marsh ◽

G. Rodriguez ◽

G. C. Bazan

Keyword(s):

Data Sets ◽

Crystal Data ◽

Asymmetric Unit ◽

Full Data ◽

Threefold Axis ◽

Data Set ◽

Group 4 ◽

Group 5

The six-electron-donating ligand tribenzylidenemethandiide has been used to form a tantalum (group 5) mimic, (η 5-cyclopentadienyl)(η 4-tribenzylidenemethandiide)dimethyltantalum, of a group 4 bent metallocene. The material crystallizes with two molecules in the asymmetric unit with quite different packing arrangements, although the overall structures of the two are similar. The Cp and methyl ligands are disordered about a threefold axis. Crystal data: [Ta{(C7H6)3C}(C5H5)(CH3), trigonal P31c, with a = 12.681 (3), c = 16.124 (5) Å, V = 2245.5 (7) Å3, T = 293 K, Z = 4, Mr = 558.47, Dx = 1.65 g cm−3, F(000) = 1104, Mo Kα, λ = 0.71073 Å, μ = 4.91 mm−1, R = 0.020 for 1319 reflections with Fo > 4σ(F o); S = 2.18. Because of crystal decay, three separate crystals were needed for a full data set. These polar (but achiral) crystals showed apparently differing amounts of inversion twinning, leading to problems in accurately merging the three data sets and refining the structure. These problems are discussed briefly.

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Data Exploration Toolkitfor serial diffraction experiments

Acta Crystallographica Section D Biological Crystallography ◽

10.1107/s1399004714025875 ◽

2015 ◽

Vol 71 (2) ◽

pp. 352-356 ◽

Cited By ~ 21

Author(s):

Oliver B. Zeldin ◽

Aaron S. Brewster ◽

Johan Hattne ◽

Monarin Uervirojnangkoorn ◽

Artem Y. Lyubimov ◽

...

Keyword(s):

Data Collection ◽

Diffraction Data ◽

Data Exploration ◽

Data Sets ◽

Significant Heterogeneity ◽

Free Electron Lasers ◽

X Ray ◽

Experimental Strategy ◽

Serial Crystallography

Ultrafast diffraction at X-ray free-electron lasers (XFELs) has the potential to yield new insights into important biological systems that produce radiation-sensitive crystals. An unavoidable feature of the `diffraction before destruction' nature of these experiments is that images are obtained from many distinct crystals and/or different regions of the same crystal. Combined with other sources of XFEL shot-to-shot variation, this introduces significant heterogeneity into the diffraction data, complicating processing and interpretation. To enable researchers to get the most from their collected data, a toolkit is presented that provides insights into the quality of, and the variation present in, serial crystallography data sets. These tools operate on the unmerged, partial intensity integration results from many individual crystals, and can be used on two levels: firstly to guide the experimental strategy during data collection, and secondly to help users make informed choices during data processing.

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