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. 2018 Sep 3;8:13123. doi: 10.1038/s41598-018-31370-0

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© The Author(s) 2018

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 license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license 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 license, visit http://creativecommons.org/licenses/by/4.0/.

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Detailed information for the retinal chromophore. (a) The F_obs − F_calc omit map of retinal and the side chain atoms of Lys216 is shown at contour levels of 4σ (gray) and 7σ (magenta). (b) Plot for the helicity angle along the polyene chain of retinal. The helicity for this study is plotted in green. Bars represent standard deviations derived from the three structures. In addition, helicities for 1C3W¹⁰ and a DFT/MM optimized structure²⁶ are plotted magenta and gray, respectively. The helicity η, a twist from the planar conformation, is calculated with the relation, η(°) = (180 − torsion) × (−1)ⁿ (ref.²⁶). (c) Interactions between retinal and the protein environment. Side chains of residues within 3.5 Å from retinal are shown as semi-transparent spheres. (d) The top view of (c).