MRCZ - A file format for cryo-TEM data with fast compression

A standard data format for 3DED/MicroED

Electron diffraction from three dimensional crystals, as a technique for solving molecular structures, is rapidly increasing in popularity. The development of methodology and software has borrowed, to great effect, from macromolecular X-ray crystallography. However, standardization lags behind the development of the technique, and practitioners are forced to work with inadequate data formats that are unable to capture a full description of their experiments. This creates obstacles that are increasingly difficult to overcome as experiments become ever faster and the need for data autoprocessing becomes more pressing. We present a data format standard based on best practice from macromolecular crystallography and demonstrate how the adoption of this standard enabled autoprocessing of datasets collected with a high-throughput detector system.

Precision requirements and data compression in CryoEM/CryoET

With larger, higher speed detectors and improved automation, individual CryoEM instruments are capable of producing a prodigious amount of data each day, which must then be stored, processed and archived. While it has become routine to use lossless compression on raw counting-mode movies, the averages which result after correcting these movies no longer compress well. These averages could be considered sufficient for long term archival, yet they are conventionally stored with 32 bits of precision, despite high noise levels. Derived images are similarly stored with excess precision, providing an opportunity to decrease project sizes and improve processing speed. We present a simple argument based on propagation of uncertainty for safe bit truncation of flat-fielded images combined with lossless compression. The same method can be used for most derived images throughout the processing pipeline. We test the proposed strategy on two standard, data-limited CryoEM data sets, demonstrating that these limits are safe for real-world use. We find that 5 bits of precision is sufficient for virtually any raw CryoEM data and that 8-12 bits is sufficient for intermediate averages or final 3-D structures. Additionally, we detail and recommend specific rules for discretization of data as well as a practical compressed data representation that is tuned to the specific needs of CryoEM.

A data reduction and compression description for high throughput time-resolved electron microscopy

Fast, direct electron detectors have significantly improved the spatio-temporal resolution of electron microscopy movies. Preserving both spatial and temporal resolution in extended observations, however, requires storing prohibitively large amounts of data. Here, we describe an efficient and flexible data reduction and compression scheme (ReCoDe) that retains both spatial and temporal resolution by preserving individual electron events. Running ReCoDe on a workstation we demonstrate on-the-fly reduction and compression of raw data streaming off a detector at 3 GB/s, for hours of uninterrupted data collection. The output was 100-fold smaller than the raw data and saved directly onto network-attached storage drives over a 10 GbE connection. We discuss calibration techniques that support electron detection and counting (e.g., estimate electron backscattering rates, false positive rates, and data compressibility), and novel data analysis methods enabled by ReCoDe (e.g., recalibration of data post acquisition, and accurate estimation of coincidence loss).

The use of electron detectors with high spatio-temporal resolution is limited by the large amounts of data generated. Here, the authors describe ReCoDe, a data reduction and compression scheme, that preserves individual electron events, and enable on-the-fly reduction and compression of raw data.

Retrieving high-resolution information from disordered 2D crystals by single-particle cryo-EM

Electron crystallography can reveal the structure of membrane proteins within 2D crystals under close-to-native conditions. High-resolution structural information can only be reached if crystals are perfectly flat and highly ordered. In practice, such crystals are difficult to obtain. Available image unbending algorithms correct for disorder, but only perform well on images of non-tilted, flat crystals, while out-of-plane distortions are not addressed. Here, we present an approach that employs single-particle refinement procedures to locally unbend crystals in 3D. With this method, density maps of the MloK1 potassium channel with a resolution of 4 Å were obtained from images of 2D crystals that do not diffract beyond 10 Å. Furthermore, 3D classification allowed multiple structures to be resolved, revealing a series of MloK1 conformations within a single 2D crystal. This conformational heterogeneity explains the poor diffraction observed and is related to channel function. The approach is implemented in the FOCUS package.

The structural organization of substrate loading in iterative polyketide synthases

Polyketide synthases (PKSs) are microbial multienzymes for the biosynthesis of biologically potent secondary metabolites. Polyketide production is initiated by the loading of a starter unit onto an integral acyl carrier protein (ACP) and its subsequent transfer to the ketosynthase (KS). Initial substrate loading is achieved either by multidomain loading modules or by the integration of designated loading domains, such as starter unit acyltransferases (SAT), whose structural integration into PKS remains unresolved. A crystal structure of the loading/condensing region of the nonreducing PKS CTB1 demonstrates the ordered insertion of a pseudodimeric SAT into the condensing region, which is aided by the SAT-KS linker. Cryo-electron microscopy of the post-loading state trapped by mechanism-based crosslinking of ACP to KS reveals asymmetry across the CTB1 loading/-condensing region, in accord with preferential 1:2 binding stoichiometry. These results are critical for re-engineering the loading step in polyketide biosynthesis and support functional relevance of asymmetric conformations of PKSs.