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Data for Atomic structure study of the pyrochlore Yb2Ti2O7 and its relationship with low-temperature magnetic order Ali Mostaed (7206197) Geetha Balakrishnan (5439575) Martin R. Lees (1896280) Yukio Yasui (3249738) Lieh-Jeng Chang (24790642) R. Beanland (5088149) Solid State Chemistry Condensed matter -- Magnetic properties Scanning transmission electron microscopy Migrated from ePrints There has been great interest in the magnetic behavior of pyrochlore oxides with the general formula A2B2O7, in which rare-earth (A), and transition metal (B) cations are ordered on separate interpenetrating lattices of corner-sharing tetrahedra. Such materials exhibit behaviors including quantum spin-ice, (quantum) spin-liquid, and ordered magnetic ground states. Yb2Ti2O7 lies on the boundary between a number of competing magnetic ground states. Features in the low-temperature specific heat capacity that vary in sharpness and temperature from sample to sample suggest that in some cases the magnetic moments order, while in others the moments remain dynamic down to temperatures as low as ~16 mK. In this work, three different Yb2Ti2O7 samples, all grown by the optical floating zone technique but exhibiting quite different heat capacity behavior, are studied by aberration-corrected scanning transmission microscopy (STEM). Atomic-scale energy-dispersive X-ray analysis shows that a crystal with no specific heat anomaly has substitution of Yb atoms on Ti sites (‘stuffing’). We show that the detailed intensity distribution around the visible atomic columns in annular dark field STEM images is sensitive to the presence of nearby atoms of low atomic number (in this case oxygen) and find significant differences between the samples that correlates both with their magnetic behavior and measurements of Ti oxidation state using electron energy loss spectroscopy. These measurements support the view that the magnetic ground state of Yb2Ti2O7 is extremely sensitive to disorder.<br><br>Protein structures as generated by the flexibility analysis The dataset contains subfolders, named after the PDB codes of the proteins such as “ERp57” or classes such as “hPDI” (human PDI). Typically, these folders contain a few files related to running FIRST and/or normal mode analysis. A file called [PDBcode]_FH.ps will be a rigidity dilution plot. In addition, two subfolders: “Runs” and “Modes”. The “Modes” folder just contains the normal mode vectors for modes 07 – 11. The “Runs” folder contains a folder called “2.0” (all simulations included here have been run at Ecut = - 2.0 kcal/mol.) The Runs/2.0/ folder contains a set of folders called e.g. Mode07-pos or Mode11-neg. The contents of these are the pdb files saved from the FRODA runs in the mode and direction given in the folder name. Other files are standard files produced form running FIRST/FRODA and possibly some extra ones we’ve generated in the process of analyzing the FRODA runs. Some of the folders contain additional subfolders when the initial PDB structure contains two protein molecules in the crystal unit, and we have a folder called e.g. 4EKZ_chainA, which itself will contain the Runs/2.0/Mode directories. Movies The files named *-movies.zip contain movies made from the conformers in the other folders. After unzipping, one gets a complete set of such movies, made with Pymol, for Ecut= -1.0 and -2.0, modes 7 to 11 and in positive and negative direction. Also, all movies have been made with “cartoon” and “sphere” setting in pymol. Additional information Here is a list of some of the key residues used in generating many of the graphs. • Central atoms to represent the domain: 2B5E: Ala86, Val191, Val291, Ala433 (CA atom numbers 981, 2583, 4147, 6382). 3BOA: same as 2B5E (CA atom numbers 946, 2547, 4111, 6344). 3F8U: Lys82, Ala185, Ala300, Ala432. (CA atom numbers 858, 2420, 4279, 6369) 4EKZ: Ala80, Gly185, Ile289, Ala 423. (CA atom numbers 1175, 2739, 4331, 6508) 4EL1: Same as 4EKZ (CA atom numbers 961, 2525, 4127, 6270) (=4EL1chainA) • Active site residues: yPDI: Cys61 and Cys406 (first C residue in CGHC bit). (b and bp "active sites" are 170 and 266) hPDI: Cys53 and Cys397. (b and bp "active sites" are D167 and D267) (4EL1_chainA atom numbers of these are 564, 2256, 3778, 5855) (4EKZ atom numbers of these are 776, 2470, 3982, 6093) ERp57: Cys57 and Cys406. (b and bp "active sites" are E166 and A273) (ERp57_chain A atom numbers of these are 408, 2112, 3828, 5952). • Four atoms per domain (central to the beta-sheets, like in the yPDI paper) Residue numbers are given (alpha-carbon atoms were used in calculations). yPDI: a: 53, 55, 108, 110. b: 163, 165, 202, 204. bp: 260, 262, 314, 316. ap: 398, 400, 453, 455. yPDI fragment (2K18): b: 28, 30, 74, 76. bp: 128, 130, 186, 188. hPDI AND ERp57: a: 49, 51, 103, 105. b: 156, 158, 202, 204. bp: 261, 263, 326, 328. ap: 398, 400, 453, 455. ERp44: a: 21, 23, 81, 83. b: 134, 136, 179, 181. bp: 235, 237, 292, 294. ERp27: b: 59, 61, 106, 108. bp: 164, 166, 222, 224. • Missing residues In hPDI there are some missing residues in the PDB files. This is true for both structures, although different residues are missing in each case. hPDI reduced full length. PDB code 4EKZ 1 chain. Missing residues: 322,323, 240-244 (inclusive) Residue 321 and 324 have CA atoms 4861 and 4877. MAX dist in all ten mode directions is 9.92116 Residue 239 and 245 have CA atoms 3611 and 3627. MAX dist in all ten mode directions is 19.8494 hPDI oxidized fill length. PDB code 4EL1. 2 chains, A and B Missing residues: 320-323, 250-254. Residue 249 and 255 have CA atoms 3557 and 3578. MAX dist in all ten mode directions is 10.2586 Residue 319 and 324 have CA atoms 4624 and 4639. MAX dist in all ten mode directions is 6.509444 From part of a protein with 2 CA atoms in a line (an N terminus), the separation of CAs there is 3.87. Between atom 4681 and 4877 there are 3 such separations => max possible is 3*3.87 = 11.61. Between atom 3611 and 3627 there are 6 such separations => max possible is 6*3.87 = 23.22. Between atom 3557 and 3578 there are 6 such separations => max possible is 6*3.87 = 23.22. Between atom 4626 and 4639 there are 5 such separations => max possible is 5*3.87 = 19.35. 2017-03-07T00:00:00Z Dataset Dataset 10.82444/warw.33735415.v1 https://figshare.com/articles/dataset/Data_for_Atomic_structure_study_of_the_pyrochlore_Yb2Ti2O7_and_its_relationship_with_low-temperature_magnetic_order/33735415 CC BY 4.0