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      Multi-wavelength anomalous diffraction de novo phasing using a two-colour X-ray free-electron laser with wide tunability

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          Abstract

          Serial femtosecond crystallography at X-ray free-electron lasers (XFELs) offers unprecedented possibilities for macromolecular structure determination of systems prone to radiation damage. However, de novo structure determination, i.e., without prior structural knowledge, is complicated by the inherent inaccuracy of serial femtosecond crystallography data. By its very nature, serial femtosecond crystallography data collection entails shot-to-shot fluctuations in X-ray wavelength and intensity as well as variations in crystal size and quality that must be averaged out. Hence, to obtain accurate diffraction intensities for de novo phasing, large numbers of diffraction patterns are required, and, concomitantly large volumes of sample and long X-ray free-electron laser beamtimes. Here we show that serial femtosecond crystallography data collected using simultaneous two-colour X-ray free-electron laser pulses can be used for multiple wavelength anomalous dispersion phasing. The phase angle determination is significantly more accurate than for single-colour phasing. We anticipate that two-colour multiple wavelength anomalous dispersion phasing will enhance structure determination of difficult-to-phase proteins at X-ray free-electron lasers.

          Abstract

          X-ray free-electron lasers produce bright femtosecond X-ray pulses. Here, the authors use a two-colour X-ray free-electron laser beam for simultaneous two-wavelength data collection and show that protein structures can be determined with multiple wavelength anomalous dispersion phasing, which is important for difficult-to-phase projects.

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          Automated structure solution with autoSHARP.

          We present here the automated structure solution pipeline "autoSHARP." It is built around the heavy-atom refinement and phasing program SHARP, the density modification program SOLOMON, and the ARP/wARP package for automated model building and refinement (using REFMAC). It allows fully automated structure solution, from merged reflection data to an initial model, without any user intervention. We describe and discuss the preparation of the user input, the data flow through the pipeline, and the various results obtained throughout the procedure.
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            Native structure of photosystem II at 1.95 Å resolution viewed by femtosecond X-ray pulses.

            Photosynthesis converts light energy into biologically useful chemical energy vital to life on Earth. The initial reaction of photosynthesis takes place in photosystem II (PSII), a 700-kilodalton homodimeric membrane protein complex that catalyses photo-oxidation of water into dioxygen through an S-state cycle of the oxygen evolving complex (OEC). The structure of PSII has been solved by X-ray diffraction (XRD) at 1.9 ångström resolution, which revealed that the OEC is a Mn4CaO5-cluster coordinated by a well defined protein environment. However, extended X-ray absorption fine structure (EXAFS) studies showed that the manganese cations in the OEC are easily reduced by X-ray irradiation, and slight differences were found in the Mn-Mn distances determined by XRD, EXAFS and theoretical studies. Here we report a 'radiation-damage-free' structure of PSII from Thermosynechococcus vulcanus in the S1 state at a resolution of 1.95 ångströms using femtosecond X-ray pulses of the SPring-8 ångström compact free-electron laser (SACLA) and hundreds of large, highly isomorphous PSII crystals. Compared with the structure from XRD, the OEC in the X-ray free electron laser structure has Mn-Mn distances that are shorter by 0.1-0.2 ångströms. The valences of each manganese atom were tentatively assigned as Mn1D(III), Mn2C(IV), Mn3B(IV) and Mn4A(III), based on the average Mn-ligand distances and analysis of the Jahn-Teller axis on Mn(III). One of the oxo-bridged oxygens, O5, has significantly longer distances to Mn than do the other oxo-oxygen atoms, suggesting that O5 is a hydroxide ion instead of a normal oxygen dianion and therefore may serve as one of the substrate oxygen atoms. These findings provide a structural basis for the mechanism of oxygen evolution, and we expect that this structure will provide a blueprint for the design of artificial catalysts for water oxidation.
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              Substructure solution with SHELXD.

              Iterative dual-space direct methods based on phase refinement in reciprocal space and peak picking in real space are able to locate relatively large numbers of anomalous scatterers efficiently from MAD or SAD data. Truncation of the data at a particular resolution, typically in the range 3.0-3.5 A, can be critical to success. The efficiency can be improved by roughly an order of magnitude by Patterson-based seeding instead of starting from random phases or sites; Patterson superposition methods also provide useful validation. The program SHELXD implementing this approach is available as part of the SHELX package.
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                Author and article information

                Contributors
                Ilme.Schlichting@mpimf-heidelberg.mpg.de
                Journal
                Nat Commun
                Nat Commun
                Nature Communications
                Nature Publishing Group UK (London )
                2041-1723
                27 October 2017
                27 October 2017
                2017
                : 8
                : 1170
                Affiliations
                [1 ]ISNI 0000 0001 2202 0959, GRID grid.414703.5, Max-Planck-Institut für medizinische Forschung, ; Jahnstrasse 29, Heidelberg, 69120 Germany
                [2 ]ISNI 0000 0001 2248 6943, GRID grid.69566.3a, Institute of Multidisciplinary Research for Advanced Materials, , Tohoku University, ; Sendai, 980-8577 Japan
                [3 ]RIKEN SPring-8 Center, Kouto 1-1-1, Sayo, Hyogo, 679-5148 Japan
                [4 ]ISNI 0000 0004 0372 2033, GRID grid.258799.8, Department of Cell Biology, Graduate School of Medicine, , Kyoto University, ; Yoshidakonoe-cho, Sakyo-ku, Kyoto, 606-8501 Japan
                [5 ]ISNI 0000 0001 2170 091X, GRID grid.410592.b, Japan Synchrotron Radiation Research Institute, ; 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5198 Japan
                Author information
                http://orcid.org/0000-0002-2472-1684
                Article
                754
                10.1038/s41467-017-00754-7
                5660077
                29079797
                3b218594-8308-421a-98bf-178709f4f104
                © The Author(s) 2017

                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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                : 26 May 2017
                : 25 July 2017
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