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Synergy s

Manufactured by Rigaku

The Synergy S is a high-performance X-ray diffractometer designed for a wide range of crystallographic applications. It features a powerful X-ray source, an advanced detector, and a versatile sample stage, enabling accurate and efficient data collection.

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6 protocols using synergy s

1

3D Diffuse Scattering Data Reconstruction

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X-ray experiments were performed on a Rigaku Synergy S diffractometer equipped with an Eiger 1 M detector using Mo radiation, ( sinθmax/λ=1.28 Å–1). To avoid possible fluorescence a threshold of 17.4 keV was used on the detector. Simple ω -scans with 0.5° step widths and 120 s exposure time were taken. The crystal was kept at ambient conditions. 3D diffuse scattering data was reconstructed on a 501×501×501 voxel reciprocal space grid ( 10h,k,l10 ) using the orientation matrix provided by CrysAlis Pro56 and custom Python scripts using Meerkat57 .
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2

Lanthanide Complex Structural Analyses

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Elemental analyses (C, H, and N) were performed using a vario EL (Elementar Analysensysteme GmbH Co.). 1H-NMR spectra were collected on a JEOL JNM-ECP 500. UV spectra and luminescence spectra were recorded on a Shimadzu UV-3600S and a Horiba Jobin Yvon Fluorolog 3-22, respectively. Absolute luminescence quantum yield values were measured using a Hamamatsu Photonics K.K. C9920-02 for the UV-vis wavelength region and C13534 for NIR. Structural analyses of a series of LnL complexes were performed using a Rigaku Synergy S and XtaLAB mini II, Rigaku Oxford diffractometer with Mo Kα radiation (λ = 0.71073 Å). The structures were solved by direct methods and refined on F2 by a full-matrix least-squares method using the SHELXTL-97 program: CCDC 2144933 (at 90 K) and 2144934 (at 300 K) for EuL, 2144935 for GdL, 2144936 for TbL, 2144931 for NdL, 2144932 for SmL, 2144937 for DyL, and 2144938 for YbL. Synchrotron X-ray diffraction data were collected at the beam line BL02B2 (λ = 0.998983 Å) in SPring-8. The sample was held in a glass capillary (Markröhrchenaus Glas, 0.3 mm, Hilgenberg Co.)
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3

Single Crystal X-ray Diffraction of L-Selenocysteine Seleninic Acid

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The single crystal X‐ray diffraction data for L‐selenocysteine seleninic acid (1
a) were measured on a Rigaku Synergy‐S diffractometer microsource Cu−Kα radiation (λ=1.54184 Å) at 123 K. Data processing was conducted using CrysAlisPro software suite.[81] The structure was solved using direct methods with SHELXT[82] and refined using full‐matrix least‐squares methods against F2 with SHELXL‐2018,[83] (link) in conjunction with the Olex2[84] graphical user interface. All hydrogen atoms were placed in calculated positions using the riding model. Crystal Data for C3H9NO5Se (M =218.07 g/mol): orthorhombic, space group P212121 (no. 19), a=5.93050(10) Å, b=10.72050(10) Å, c=11.06300(10) Å, V=703.363(15) Å3, Z=4, T=122.99(10) K, μ(CuKα)=7.091 mm−1, Dcalc=2.059 g/cm3, 4056 reflections measured (11.494°≤2θ≤151.5°), 1318 unique (Rint=0.0183, Rsigma=0.0173) which were used in all calculations. The final R1 was 0.0168 (I>2σ(I)) and wR2 was 0.0445 (all data).
The data can be obtained free of charge from The Cambridge Crystallographic Data Centre via www.ccdc.cam.ac.uk/data_request/cif. (CCDC number: 2044358)
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4

Crystallization and X-ray Structure Analysis

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Crystals for X-ray structure analysis were grown using saturated solutions in acetonitrile (1), or THF-C6D6 (2). Crystals 1 and 2 were immersed in paratone, and were measured on a Rigaku SynergyS diffractometer. The SynergyS operated using microsource Cu-Kα radiation (λ = 1.54184 Å) at 123 K. Data processing was conducted using the CrysAlisPro.55 software suite [46 ]. Structural solutions were obtained by ShelXT [47 (link)] and refined using full-matrix least-squares methods against F2 using SHELXL [48 (link)], in conjunction with Olex2 [49 (link)] graphical user interface. All hydrogen atoms were placed in calculated positions using the riding model.
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5

Single Crystal X-ray Diffraction

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Single crystals were obtained by ether diffusion into acetone solutions of [1](CF3SO3)2 and [2](CF3SO3)2, a methanol solution of [3](CF3SO3)2, a nitromethane solution of [4](PF6)2 and a methanol solution of [5](PF6)2 at room temperature. Intensity data of X-ray crystallography were measured at 298 K on a Rigaku Synergy-S diffractometer using multi-layer mirror monochromated CuKα radiation (1.54184 Å). All calculations were carried out using Olex2 1.2. Structures were solved by direct methods, expected using Fourier techniques and refined using full-matrix least-squares techniques on F2 using SHELXL97 or SHELXT Version 2014/5. Structural Figures of thermal ellipsoid plots were made by Ortep-3 for Windows (L. J. Farrugia, J. Appl. Crystallogr., 2012, 45, 849–854). ESI.
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6

Protein Crystallization and Structure Determination

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Proteins (in the concentration range 10–15 mg ml−1) were crystallized by vapor diffusion in hanging drops at 20°C. Crystals were grown from solutions consisting of 20–30% PEG 4000 or PEG 6000, 0.2 M MgCl2 in 100 mM Tris–HCl pH 8.5. X-ray diffraction data were collected using synchrotron radiation on the EMBL beamlines at the PETRA III storage ring at DESY in Hamburg or using Cu Kα radiation from a home-source Synergy-S or Synergy-R XtaLAB (Rigaku) generator. The diffraction images were processed and scaled using the CrysAlisPro (Rigaku), CCP4 (Winn et al., 2011 ▸ ) or XDS (Kabsch, 2010 ▸ ) packages. Structures were solved by molecular replacement using Phaser (McCoy et al., 2007 ▸ ) and were refined with REFMAC5 (Murshudov et al., 2011 ▸ ) using anisotropic or TLS protocols. The electron-density maps were inspected in Coot (Emsley et al., 2010 ▸ ). All crystal structures were standardized in the unit cell using the ACHESYM server (Kowiel et al., 2014 ▸ ). All data-collection and structure-refinement statistics are summarized in Table 2. The structures were analyzed and visualized using PyMOL. Together with the series of crystal structures of the RDM1 mutants, the structure of the WT protein (without bound ligand) was determined at 1.55 Å resolution.
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