Abstract
The web-based IceBear software is a versatile tool to monitor the results of crystallization experiments and is designed to facilitate supervisor and student communications. It also records and tracks all relevant information from crystallization setup to PDB deposition in protein crystallography projects. Fully automated data collection is now possible at several synchrotrons, which means that the number of samples tested at the synchrotron is currently increasing rapidly. Therefore, the protein crystallography research communities at the University of Oulu, Weizmann Institute of Science and Diamond Light Source have joined forces to automate the uploading of sample metadata to the synchrotron. In IceBear, each crystal selected for data collection is given a unique sample name and a crystal page is generated. Subsequently, the metadata required for data collection are uploaded directly to the ISPyB synchrotron database by a shipment module, and for each sample a link to the relevant ISPyB page is stored. IceBear allows notes to be made for each sample during cryocooling treatment and during data collection, as well as in later steps of the structure determination. Protocols are also available to aid the recycling of pins, pucks and dewars when the dewar returns from the synchrotron. The IceBear database is organized around projects, and project members can easily access the crystallization and diffraction metadata for each sample, as well as any additional information that has been provided via the notes. The crystal page for each sample connects the crystallization, diffraction and structural information by providing links to the IceBear drop-viewer page and to the ISPyB data-collection page, as well as to the structure deposited in the Protein Data Bank.
Highlights
Data collection at synchrotrons has generally become a routine step in the protein structure-determination pipeline (Helliwell, 2017; Dauter & Wlodawer, 2016; Owen et al, 2016; Grimes et al, 2018) that starts with crystallization of the protein and results in the deposition of its structure and experimental structure factors in the Protein Data Bank (PDB)
For ISPyB the sample name can be at most 45 characters, but a maximal length of 27 characters is recommended as different synchrotrons have different implementations
Efficient exchange of the crystal metadata between the home laboratory and synchrotron, as implemented in the IceBear software (Fig. 1), is of critical importance. This makes it easy to address questions related to data collection and data processing of a sample when refining its structure and to correlate this information with the experimental details of the crystallization and crystalhandling experiments (Fig. 10, Supplementary Fig. S4)
Summary
Data collection at synchrotrons has generally become a routine step in the protein structure-determination pipeline (Helliwell, 2017; Dauter & Wlodawer, 2016; Owen et al, 2016; Grimes et al, 2018) that starts with crystallization of the protein and results in the deposition of its structure and experimental structure factors in the Protein Data Bank (PDB). In Europe, the Diamond Light Source (DLS) in the UK and the European Synchrotron Radiation Facility (ESRF) in France have developed powerful data-processing pipelines by which the collected data can be processed automatically (Monaco et al, 2013; Materlik et al, 2015). To address the the relevant metadata such as sequence, model structure and needs of crystallization home laboratories, software has been ligand are available. Efficient use of this impressive tech- developed by the University of Oulu and DLS, which is nology by home laboratories typically located on campuses of referred to as IceBear (Integrated Crystal-data-tracking universities, research institutes or (biotech) industries, on sites Enhancing Biochemistry Education And Research; https://.
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callMore From: Acta Crystallographica Section D Structural Biology
Disclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
