Autoindexing the diffraction patterns from crystals with a pseudotranslation

Ontogenetic variability in crystallography and mosaicity of conodont apatite: implications for microstructure, palaeothermometry and geochemistry

X-ray diffraction data from Silurian conodonts belonging to various developmental stages of the species Dapsilodus obliquicostatus demonstrate changes in crystallography and degree of nanocrystallite ordering (mosaicity) in both lamellar crown tissue and white matter. The exclusive use of a single species in this study, combined with systematic testing of each element type at multiple locations, provided insight into microstructural and crystallographic differentiation between element type (Sa , Sb -c , M) as well as between juveniles and adults. A relative increase in the unit cell dimensions a/c ratio of nanocrystallites during growth was apparent in areas demonstrating single-crystal behaviour, but no such relationship was seen in dominantly polycrystalline areas. Systematic variations in mosaicity were identified, with mosaicity (as a proxy for disorder) increasing during growth, as well as along elements from tip to base. These results provide potential insight into the integrity of conodont apatite as a recorder of palaeoseawater chemistry, as well as demonstrate the need to consider the influence of ontogeny and element type on the use of conodonts in palaeothermometry and geochemical investigations.

XGANDALF - extended gradient descent algorithm for lattice finding

Serial crystallography records still diffraction patterns from single, randomly oriented crystals, then merges data from hundreds or thousands of them to form a complete data set. To process the data, the diffraction patterns must first be indexed, equivalent to determining the orientation of each crystal. A novel automatic indexing algorithm is presented, which in tests usually gives significantly higher indexing rates than alternative programs currently available for this task. The algorithm does not require prior knowledge of the lattice parameters but can make use of that information if provided, and also allows indexing of diffraction patterns generated by several crystals in the beam. Cases with a small number of Bragg spots per pattern appear to particularly benefit from the new approach. The algorithm has been implemented and optimized for fast execution, making it suitable for real-time feedback during serial crystallography experiments. It is implemented in an open-source C++ library and distributed under the LGPLv3 licence. An interface to it has been added to the CrystFEL software suite.

Challenge data set for macromolecular multi-microcrystallography

A synthetic data set demonstrating a particularly challenging case of indexing ambiguity in the context of radiation damage was generated. This set shall serve as a standard benchmark and reference point for the ongoing development of new methods and new approaches to robust structure solution when single-crystal methods are insufficient. Of the 100 short wedges of data, only the first 36 are currently necessary to solve the structure by `cheating', or using the correct reference structure as a guide. The total wall-clock time and number of crystals required to solve the structure without cheating is proposed as a metric for the efficacy and efficiency of a given multi-crystal automation pipeline.

Automatic crystal centring procedure at the SSRF macromolecular crystallography beamline

X-ray diffraction is a common technique for determining crystal structures. The average time needed for the solution of a protein structure has been drastically reduced by a number of recent experimental and theoretical developments. Since high-throughput protein crystallography benefits from full automation of all steps that are carried out on a synchrotron beamline, an automatic crystal centring procedure is important for crystallographic beamlines. Fully automatic crystal alignment involves the application of optical methods to identify the crystal and move it onto the rotation axis and into the X-ray beam. Crystal recognition has complex dependencies on the illumination, crystal size and viewing angles due to effects such as local shading, inter-reflections and the presence of antifreezing elements. Here, a rapid procedure for crystal centring with multiple cameras using region segment thresholding is reported. Firstly, a simple illumination-invariant loop recognition and classification model is used by slicing a low-magnification loop image into small region segments, then classifying the loop into different types and aligning it to the beam position using feature vectors of the region segments. Secondly, an edge detection algorithm is used to find the crystal sample in a high-magnification image using region segment thresholding. Results show that this crystal centring method is extremely successful under fluctuating light states as well as for poorly frozen and opaque samples. Moreover, this crystal centring procedure is successfully integrated into the enhanced Blu-Ice data collection system at beamline BL17U1 at the Shanghai Synchrotron Radiation Facility as a routine method for an automatic crystal screening procedure.

Tightly integrated single- and multi-crystal data collection strategy calculation and parallelized data processing in JBluIce beamline control system

The calculation of single- and multi-crystal data collection strategies and a data processing pipeline have been tightly integrated into the macromolecular crystallographic data acquisition and beamline control software JBluIce. Both tasks employ wrapper scripts around existing crystallographic software. JBluIce executes scripts through a distributed resource management system to make efficient use of all available computing resources through parallel processing. The JBluIce single-crystal data collection strategy feature uses a choice of strategy programs to help users rank sample crystals and collect data. The strategy results can be conveniently exported to a data collection run. The JBluIce multi-crystal strategy feature calculates a collection strategy to optimize coverage of reciprocal space in cases where incomplete data are available from previous samples. The JBluIce data processing runs simultaneously with data collection using a choice of data reduction wrappers for integration and scaling of newly collected data, with an option for merging with pre-existing data. Data are processed separately if collected from multiple sites on a crystal or from multiple crystals, then scaled and merged. Results from all strategy and processing calculations are displayed in relevant tabs of JBluIce.

Purification, crystallization and room-temperature X-ray diffraction of inositol dehydrogenase LcIDH2 from Lactobacillus casei BL23

Lactobacillus casei BL23 contains two genes, iolG1 and iolG2, homologous with inositol dehydrogenase encoding genes from many bacteria. Inositol dehydrogenase catalyzes the oxidation of inositol with concomitant reduction of NAD+. The protein encoded by iolG2, LcIDH2, has been purified to homogeneity, crystallized and cryoprotected for diffraction at 77 K. The crystals had a high mosaicity and poor processing statistics. Subsequent diffraction measurements were performed without cryoprotectant at room temperature. These crystals were radiation-resistant and a full diffraction data set was collected at room temperature to 1.6 Å resolution.

Autoindexing diffraction images with iMosflm

The principles of one-dimensional FFT-based autoindexing of diffraction images are described together with practical issues that may arise. A procedure for indexing multiple lattices as implemented in iMosflm is presented.

An overview of autoindexing diffraction images based on one-­dimensional fast Fourier transforms is presented. The implementation of the algorithm in the Mosflm/iMosflm program suite is described with a discussion of practical issues that may arise and ways of assessing the success or failure of the procedure. Recent developments allow indexing of images that show multiple lattices, and several examples demonstrate the success of this approach in real cases.

A new generation of crystallographic validation tools for the protein data bank

This report presents the conclusions of the X-ray Validation Task Force of the worldwide Protein Data Bank (PDB). The PDB has expanded massively since current criteria for validation of deposited structures were adopted, allowing a much more sophisticated understanding of all the components of macromolecular crystals. The size of the PDB creates new opportunities to validate structures by comparison with the existing database, and the now-mandatory deposition of structure factors creates new opportunities to validate the underlying diffraction data. These developments highlighted the need for a new assessment of validation criteria. The Task Force recommends that a small set of validation data be presented in an easily understood format, relative to both the full PDB and the applicable resolution class, with greater detail available to interested users. Most importantly, we recommend that referees and editors judging the quality of structural experiments have access to a concise summary of well-established quality indicators.

The JCSG high-throughput structural biology pipeline

The Joint Center for Structural Genomics high-throughput structural biology pipeline has delivered more than 1000 structures to the community over the past ten years. The JCSG has made a significant contribution to the overall goal of the NIH Protein Structure Initiative (PSI) of expanding structural coverage of the protein universe, as well as making substantial inroads into structural coverage of an entire organism. Targets are processed through an extensive combination of bioinformatics and biophysical analyses to efficiently characterize and optimize each target prior to selection for structure determination. The pipeline uses parallel processing methods at almost every step in the process and can adapt to a wide range of protein targets from bacterial to human. The construction, expansion and optimization of the JCSG gene-to-structure pipeline over the years have resulted in many technological and methodological advances and developments. The vast number of targets and the enormous amounts of associated data processed through the multiple stages of the experimental pipeline required the development of variety of valuable resources that, wherever feasible, have been converted to free-access web-based tools and applications.

Autoindexing with outlier rejection and identification of superimposed lattices

Constructing a model lattice to fit the observed Bragg diffraction pattern is straightforward for perfect samples, but indexing can be challenging when artifacts are present, such as poorly shaped spots, split crystals giving multiple closely aligned lattices and outright superposition of patterns from aggregated microcrystals. To optimize the lattice model against marginal data, refinement can be performed using a subset of the observations from which the poorly fitting spots have been discarded. Outliers are identified by assuming a Gaussian error distribution for the best-fitting spots and points diverging from this distribution are culled. The set of remaining observations produces a superior lattice model, while the rejected observations can be used to identify a second crystal lattice, if one is present. The prevalence of outliers provides a potentially useful measure of sample quality. The described procedures are implemented for macromolecular crystallography within the autoindexing program labelit.index (http://cci.lbl.gov/labelit).