9CQ0

Event-based electron counting microED structure of thiostrepton from a single crystal

Summary for 9CQ0

• Entry DOI: 10.2210/pdb9cq0/pdb
• Related PRD ID: PRD_000223
• Descriptor: Thiostrepton (2 entities in total)
• Functional Keywords: cyclic, macrocycle, antibiotic
• Biological source: Streptomyces azureus
• Total number of polymer chains: 1
• Total formula weight: 1805.98

Authors

Vlahakis, N.W.,Qu, S.,Richards, L.S.,deMoraes, L.S.,Nelson, H.M.,Rodriguez, J.A. (deposition date: 2024-07-18, release date: 2025-06-04)

Primary citation

Vlahakis, N.,Qu, S.,Richards, L.S.,Moraes, L.S.,Cascio, D.,Nelson, H.M.,Rodriguez, J.A.
Fast event-based electron counting for small-molecule structure determination by MicroED.
Acta Crystallogr.,Sect.C, 81:116-130, 2025

PubMed Abstract: Electron counting helped realize the resolution revolution in single-particle cryoEM and is now accelerating the determination of MicroED structures. Its advantages are best demonstrated by new direct electron detectors capable of fast (kilohertz) event-based electron counting (EBEC). This strategy minimizes the inaccuracies introduced by coincidence loss (CL) and promises rapid determination of accurate structures. We used the Direct Electron Apollo camera to leverage EBEC technology for MicroED data collection. Given its ability to count single electrons, the Apollo collects high-quality MicroED data from organic small-molecule crystals illuminated with incident electron beam flux densities as low as 0.01-0.045 e/Å/s. Under even the lowest flux density (0.01 e/Å/s) condition, fast EBEC data produced ab initio structures of a salen ligand (268 Da) and biotin (244 Da). Each structure was determined from a 100° wedge of data collected from a single crystal in as few as 50 s, with a delivered fluence of only ∼0.5 e/Å. Fast EBEC data collected with a fluence of 2.25 or 3.33 e/Å also facilitated a 1.5 Å structure of thiostrepton (1665 Da). While refinement of these structures appeared unaffected by CL, a CL adjustment applied to EBEC data further improved the distribution of intensities measured from the salen ligand and biotin crystals. However, CL adjustment only marginally improved the refinement of their corresponding structures, signaling the already high counting accuracy of detectors with counting rates in the kilohertz range. Overall, by delivering low-dose structure-worthy data, fast EBEC collection strategies open new possibilities for high-throughput MicroED.

PubMed: 39982366
DOI: 10.1107/S2053229624012300

Experimental method

ELECTRON CRYSTALLOGRAPHY (1.5 Å)