Whole-pattern fitting technique in serial femtosecond nanocrystallography

Dilanian, Ruben A.; Williams, Sophie; Martin, Andrew V.; Streltsov, V.A.; Quiney, Harry M.

doi:10.1107/s2052252516001238

Cited by 4 publications

(10 citation statements)

References 50 publications

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“…The scattering factor of the conventional unit cell is bandwidth-limited function. We have previously [21] used this observation to express the scattering factor of the unit cell via interpolation with the shape transform of the unit cell at the Bragg sampling rate. The scattering factors from separate sub-units of the unit cell can be similarly characterised using…”

Section: Construction Of a Model For The Average Diffracted Intensitymentioning

confidence: 99%

“…This expression is used later to model the diffracted intensity distribution formed from simulated finite protein crystals with incomplete unit cells on crystal surfaces during the application of whole-pattern fitting analysis. We have previously demonstrated the feasibility of whole-pattern fitting analysis for the improved extraction of structure factor amplitudes using finite crystals [21]. In our previous work, it was shown that the diffracted intensity distribution from ideal finite crystals with whole unit cells can be written as…”

Section: The Whole-pattern Fitting Modelmentioning

confidence: 99%

“…This is also present in the model function for the diffracted intensity distribution, Equation (10), that we have demonstrated and used previously for crystals composed of whole unit cells. In our previous study [21], we chose to model these contributions with analytical peak-shape functions. Using the same approach here, Equations (19) and (20) may be equivalently written as…”

Section: The Whole-pattern Fitting Modelmentioning

confidence: 99%

“…We present a study of the accuracy of structure factor amplitudes extracted using peak integration methods compared with a new technique based on whole-pattern fitting analysis [21]. Whole-pattern fitting analysis of serial crystallography data is a technique for the iterative estimation of structure factor amplitudes via the fitting of a continuous model function to the observed diffracted intensity distribution.…”

Section: Introductionmentioning

confidence: 99%

“…In contrast, the data can be merged into higher dimensional space due to the collection of data from separate crystals. This has stimulated the development of whole-pattern fitting analysis in higher dimensional space [21]. Initial studies involved simulated, finite crystals composed entirely of whole unit cells.…”

Section: Introductionmentioning

confidence: 99%

See 4 more Smart Citations

Analysis of Diffracted Intensities from Finite Protein Crystals with Incomplete Unit Cells

et al. 2017

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Developments in experimental techniques in micro electron diffraction and serial X-ray crystallography provide the opportunity to collect diffraction data from protein nanocrystals. Incomplete unit cells on the surfaces of protein crystals can affect the distribution of diffracted intensities for crystals with very high surface-to-volume ratios. The extraction of structure factors from diffraction data for such finite protein crystals sizes is considered here. A theoretical model for the continuous diffracted intensity distribution for data merged from finite crystals with two symmetry-related sub-units of the conventional unit cell is presented. This is used to extend a whole-pattern fitting technique to account for incomplete unit cells in the extraction of structure factor amplitudes. The accuracy of structure factor amplitudes found from this whole-pattern fitting technique and from an integration approach are evaluated.

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Section: Construction Of a Model For The Average Diffracted Intensitymentioning

confidence: 99%

Section: The Whole-pattern Fitting Modelmentioning

confidence: 99%

Section: The Whole-pattern Fitting Modelmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

Analysis of Diffracted Intensities from Finite Protein Crystals with Incomplete Unit Cells

et al. 2017

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Serial electron crystallography: merging diffraction data through rank aggregation

Smeets

Wan

2017

J Appl Cryst

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Serial electron crystallography is being developed as an alternative way to collect diffraction data on beam-sensitive polycrystalline materials. Merging serial diffraction data from a large number of snapshots is difficult, and the dynamical nature of electron diffraction prevents the use of existing methods that rely on precise measurement of kinematical reflection intensities. To overcome this problem, an alternative method that uses rank aggregation to combine the rankings of relative reflection intensities from a large number of snapshots has been developed. The method does not attempt to accurately model the diffraction intensity, but instead optimizes the most likely ranking of reflections. As a consequence, the problem of scaling individual snapshots is avoided entirely, and requirements for the data quality and precision are low. The method works best when reflections can be fully measured, but the benefit over measuring partial intensities is small. Since there were no experimental data available for testing rank-based merging, the validity of the approach was assessed through a series of simulated serial electron diffraction datasets with different numbers of frames and varying degrees of errors. Several programs have been used to show that these rank-merged simulated data are good enough for ab initio structure determination using several direct methods programs.

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Beyond integration: modeling every pixel to obtain better structure factors from stills

Mendez

Bolotovsky

Bhowmick

et al. 2020

IUCrJ

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Most crystallographic data processing methods use pixel integration. In serial femtosecond crystallography (SFX), the intricate interaction between the reciprocal lattice point and the Ewald sphere is integrated out by averaging symmetrically equivalent observations recorded across a large number (104−106) of exposures. Although sufficient for generating biological insights, this approach converges slowly, and using it to accurately measure anomalous differences has proved difficult. This report presents a novel approach for increasing the accuracy of structure factors obtained from SFX data. A physical model describing all observed pixels is defined to a degree of complexity such that it can decouple the various contributions to the pixel intensities. Model dependencies include lattice orientation, unit-cell dimensions, mosaic structure, incident photon spectra and structure factor amplitudes. Maximum likelihood estimation is used to optimize all model parameters. The application of prior knowledge that structure factor amplitudes are positive quantities is included in the form of a reparameterization. The method is tested using a synthesized SFX dataset of ytterbium(III) lysozyme, where each X-ray laser pulse energy is centered at 9034 eV. This energy is 100 eV above the Yb3+ L-III absorption edge, so the anomalous difference signal is stable at 10 electrons despite the inherent energy jitter of each femtosecond X-ray laser pulse. This work demonstrates that this approach allows the determination of anomalous structure factors with very high accuracy while requiring an order-of-magnitude fewer shots than conventional integration-based methods would require to achieve similar results.

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Whole-pattern fitting technique in serial femtosecond nanocrystallography

Cited by 4 publications

References 50 publications

Analysis of Diffracted Intensities from Finite Protein Crystals with Incomplete Unit Cells

Analysis of Diffracted Intensities from Finite Protein Crystals with Incomplete Unit Cells

Serial electron crystallography: merging diffraction data through rank aggregation

Beyond integration: modeling every pixel to obtain better structure factors from stills

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