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. 2024 Mar 25;31(7):1023–1027. doi: 10.1038/s41594-024-01258-x

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© The Author(s) 2024

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.

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Extended Data Fig. 3 — (a) Processing scheme, also described in Methods. Two final reconstructions were obtained in this study: overall vPRC1:Nuc_H2Aub1 map and one side vPRC1:Nuc_H2Aub1 map from focusing refinement on one surface of the nucleosome disc (mask indicated in green). The two refined maps were further post-processed with a b-factor of −60 Å² and with DeepEMhancer. (b) Local resolution estimation of the final one side density DeepEMhancer map; RYBP/H2A acidic patch interference is highlighted showing a ~ 3.5 A resolution with colors ranging from blue (high resolution) to red (low resolution). (c) Corresponding gold-standard Fourier shell correlation (GSFSC) curves, as well as spherical distribution plot obtained from CryoSPARC (each bar has a height and color indicative of the number of particles (increasing from blue to red) in a defined orientation. (d) Representative regions of the DeepEMhancer density map for the nucleosome components (histones and DNA). DNA is in gray while histones are in pink. (e) Representative regions of the DeepEMhancer density map for the interfaces involving RYBP interactions with the H2A acidic patch. H2A is in pink while RYBP in blue.