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opencc-by-4.0Jun 2024View details →

X-Ray Diffraction data from Membrane transport protein AcrB, V612F mutant with bound minocycline, source of 9FHC structure

Crystals were grown of the membrane transport protein AcrB, V612F mutant, with bound minocycline.  X-ray diffraction data of this upload: 400 frames of 0.5° width were collected on 2007-04-30 at the X06SA beamline of Swiss Light Source at Paul-Scherrer-Institute (Switzerland). The data can be processed with XDS; XDS.INP is provided as part of the upload. The data are the basis of the PDB 9FHC structure.

opencc-by-4.0Apr 2017View details →

Comparison of X-ray crystal structures of a tetradecamer sequence d(CCCGGGTACCCGGG)2 at 1.7 Å resolution.

We presented a comparison of three different X-ray crystal structures of DNA tetradecamer sequence d(CCCGGGTACCCGGG)2 all at about 1.7 Å resolution. The sequence was designed as an attempt to form a DNA four-way junction with A-type helical arms. However, in the presence of zinc, magnesium, and in the absence of any metal ion, it does not take up the junction structure, but forms an A-type double helix. This allowed us to study possible conformational changes in the double helix due to the presence of metal ions. Upon addition of the zinc ion, there is a change in the space group from P41212 to P41. The overall conformation of the duplex remains the same. There are small changes in the interaction of the metal ions with the DNA. In the zinc-bound structure, there are two zinc ions that show direct interaction with the N7 atoms of terminal G13 bases at either end of the molecule. There are small changes in the interhelical contacts. The consequence of these differences is to break some of the symmetry and change the space group.

opencc-by-4.0Apr 2017View details →

Comparison of X-ray crystal structures of a tetradecamer sequence d(CCCGGGTACCCGGG)2 at 1.7 Å resolution.

We presented a comparison of three different X-ray crystal structures of DNA tetradecamer sequence d(CCCGGGTACCCGGG)2 all at about 1.7 Å resolution. The sequence was designed as an attempt to form a DNA four-way junction with A-type helical arms. Crystals did not have any metal ion in the crystallization solution apart from the sodium in the buffer. However, the sequence does not take up the junction structure, but forms an A-type double helix in P41212 space group.

opencc-by-4.0Apr 2017View details →

Comparison of X-ray crystal structures of a tetradecamer sequence d(CCCGGGTACCCGGG)2 at 1.7 Å resolution.

We presented a comparison of three different X-ray crystal structures of DNA tetradecamer sequence d(CCCGGGTACCCGGG)2 all at about 1.7 Å resolution. The sequence was designed as an attempt to form a DNA four-way junction with A-type helical arms. However, in the presence of magnesium, it does not take up the junction structure, but forms an A-type double helix in P41212 space group. This allowed us to study possible conformational changes in the double helix due to the presence of metal ions. Though the crystallization condition has magnesium chloride, it was not observed in the electron density map.

opencc-by-4.0Jan 2023View details →

Database of small molecule X-ray absorption spectra, featurized structures, and neural network ensembles

Companion data for arXiv preprint Uncertainty-aware predictions of molecular X-ray absorption spectra using neural network ensembles (<a href="https://arxiv.org/abs/2210.00336">https://arxiv.org/abs/2210.00336</a>), by Animesh Ghose, Mikhail Segal, Fanchen Meng, Zhu Liang, Mark S. Hybertsen, Xiaohui Qu, Eli Stavitski, Shinjae Yoo, Deyu Lu & Matthew R. Carbone. Included <ul> <li>*-XANES-*.tar.bz2: raw input/output files for all molecular simulations used in the work. These inputs and outputs correspond to the structural data in the QM9 dataset.</li> <li>ml_ready.tar.bz2: machine learning-ready data (featurized spectra). Used as input to the neural network ensembles.</li> <li>XANES-220712-ACSF-*.tar.bz2: neural network ensembles used in this work.</li> </ul> Notes <ul> <li>The FEFF9 code [J. J. Rehr, J. J. Kas, F. D. Vila, M. P. Prange, and K. Jorissen, Phys. Chem. Chem. Phys. 12, 5503 (2010)] was used to generate all X-ray absorption near-edge structure (XANES) spectra.</li> <li>All molecular structures were sourced from the QM9 database [R. Ramakrishnan, P. O. Dral, M. Rupp, and O. A. Von Lilienfeld, Sci. Data 1, 1 (2014)].</li> </ul> Funding This research is based upon work supported by the U.S. Department of Energy, Office of Science, Office Basic Energy Sciences, under Award Number FWP PS-030. This research also used theory and computational resources of the Center for Functional Nanomaterials, which is a U.S. Department of Energy Office of Science User Facility, and the Scientific Data and Computing Center, a component of the Computational Science Initiative, at Brookhaven National Laboratory under Contract No. DE-SC0012704.

opencc-by-4.0Mar 2023View details →

X-ray structures of HIV-1 protease

As of March 1, 2023, there were 233 X-ray structures of HIV-1 protease available in the RCSB PDB database (<a href="https://www.rcsb.org/">https://www.rcsb.org/</a>). Out of these structures, 219 had ligands bound in the active site while 14 did not have any ligands. To prepare the structures for analysis, we removed water, ions, and solvent molecules, extracted the ligands from the receptors, and aligned all the structures. Each HIV-1 protease structure is identified by its PDB ID (<pdbid>.pdb) while the corresponding ligand structures are named as ligs_<pdbdid>.pdb.

opencc-by-4.0Sep 2023View details →

Diffraction data underpinning the structure of StayGold determined by X-ray crystallography (PDB code 8BXT)

Raw diffraction data underpinning the crystal structure of StayGold fluorescent protein. This is the raw data underpinning PDB entry 8BXT.

opencc-by-4.0Nov 2023View details →

Dataset from the paper entitled "Complex structure of molten FLiBe (2 LiF – BeF2) examined by experimental neutron scattering, X-ray scattering, and deep neural network-based molecular dynamics"

Dataset from the paper entitled  "Complex structure of molten FLiBe (2 LiF – BeF2) examined by experimental neutron scattering, X-ray scattering, and deep neural network-based molecular dynamics". These data include experimental total scattering measurements and molecular dynamics simulations on the molten structure of FLiBe.

opencc-by-4.0Dec 2021View details →

Text-fig. 1. CT slices on Block 1. Details of the internal bone structure (a, b), teeth (b, c). Invertebrate imprints (a, c). Holes, cracks and empty cavities in both the limestone matrix and within the vertebrate fossil (b). in Hidden Treasures Uncovered: Successful Detection Of Fossils Below The Surface In Large Limestone Blocks Using A Standard Medical X-Ray Ct Scanner

Text-fig. 1. CT slices on Block 1. Details of the internal bone structure (a, b), teeth (b, c). Invertebrate imprints (a, c). Holes, cracks and empty cavities in both the limestone matrix and within the vertebrate fossil (b).

opencc-by-4.0Dec 2021View details →

Text-fig. 3. CT slices on Block 3. Invertebrate moulds (a, c) and remains of their hard skeletons (a, b). Large areas of limestone matrix hold either only a few scattered invertebrates or no fossil at all (b, c). Ring artefacts seen close to the isocentre of the scan (b, c) are a well-known phenomenon caused by the X-ray beams traversing the block at an insufficient radiation dose (as expected in such a large block of dense material), and are not part of any physical structure present therein (Triche et al. 2019). in Hidden Treasures Uncovered: Successful Detection Of Fossils Below The Surface In Large Limestone Blocks Using A Standard Medical X-Ray Ct Scanner

Text-fig. 3. CT slices on Block 3. Invertebrate moulds (a, c) and remains of their hard skeletons (a, b). Large areas of limestone matrix hold either only a few scattered invertebrates or no fossil at all (b, c). Ring artefacts seen close to the isocentre of the scan (b, c) are a well-known phenomenon caused by the X-ray beams traversing the block at an insufficient radiation dose (as expected in such a large block of dense material), and are not part of any physical structure present therein (Triche et al. 2019).

opencc-by-4.0Jan 2018View details →

X-Ray Structures of Target-Ligand Complexes Containing Compounds with Assay Interference Potential

A total of 2755 crystallographic complexes with ligands containing PAINS-defining substructures were extracted from the Protein Data Bank (PDB). PDB identifiers of these structures are made available together with the the corresponding PDB_PAINS (component identifier, aromatic nonstereo SMILES, PAINS class).

FIGURE 15 in X-ray Microanalysis and the Chemical Elemental Composition of Gorgonian and Pennatulacean Axial Structures (Anthozoa, Octocorallia)

FIGURE 15. Line chart of the between-taxa elemental weight percentage comparison of both gorgonians and sea pens

FIGURE 12 in X-ray Microanalysis and the Chemical Elemental Composition of Gorgonian and Pennatulacean Axial Structures (Anthozoa, Octocorallia)

FIGURE 12. Energy dispersive spectrometer (EDS) linescan dataset. (A) EDS linescan site of interest BSE image in a cross-sectional view of a sea pen Stylatula sp. axial skeleton acquired by INCA Energy software using same region as Figure 11, horizontal linescan through the middle of the axis was applied for EDS analysis to examine the distribution of elements along the line. Scale bar = 900 μm. (B) Element linescan result displaying grouped linescans as colored: carbon (red), oxygen (orange), fluorine (yellow), sodium (green), magnesium (light green), aluminum (bright green), silicon (aqua), sulfur (light blue), calcium (blue), strontium (pink), ytterbium (purple), iron (hot pink).

FIGURE 10 in X-ray Microanalysis and the Chemical Elemental Composition of Gorgonian and Pennatulacean Axial Structures (Anthozoa, Octocorallia)

FIGURE 10. Energy dispersive spectrometer (EDS) linescan dataset. (A) EDS linescan site of interest BSE image in a cross-sectional view of a sea pen Virgularia sp. axial skeleton acquired by INCA Energy software using same region as Figure 9, horizontal linescan through the middle of the axis was applied for EDS analysis to examine the distribution of elements along the line. (B) Element linescan result displaying grouped linescans as colored: carbon (purple), oxygen (bright green), fluorine (pink), sodium (blue), magnesium (green), sulfur (teal), chlorine (red), calcium (light green), ytterbium (gold). (C) Sum spectrum of the linescan. Scale bar = 1 mm. (D) Bar chart of the quantitative results from the sum spectrum.

FIGURE 9 in X-ray Microanalysis and the Chemical Elemental Composition of Gorgonian and Pennatulacean Axial Structures (Anthozoa, Octocorallia)

FIGURE 9. Scanning electron microscope (SEM) micrographs of a cross-sectional view of a sea pen Virgularia sp. axial skeleton. (A) In this secondary electron (SE) image a great degree of the radiating patterns well-arranged across the whole axial surface can be observed, such character is also used in the morphological phylogenetic studies of the calcaxonian gorgonians and sea pens. Scale bar = 200 μm. (B) Back-scattered electron (BSE) image. There seemed to be some chemical composition contrast appearing darker in the central portion of the axis, though several between-site area scans were performed, yet no differences in chemical composition can be found (data not shown); however, the between-site changes on weight percentage value of some elements can be detected as shown in the next Figure 10B. Scale bar = 200 μm.

FIGURE 5 in X-ray Microanalysis and the Chemical Elemental Composition of Gorgonian and Pennatulacean Axial Structures (Anthozoa, Octocorallia)

FIGURE 5. Scanning electron microscope (SEM) micrographs of a cross-sectional view of a gorgonian Ellisella sp. axial skeleton. (A) Secondary electron (SE) image. The axis of Ellisella sp. is featured by the concentric growth rings resembling that in trees, also by the slightly radiating patterns on the surface. These characters are useful for comparative morphology studies on calcaxonian gorgonians and sea pens. Scale bar = 200 μm. (B) Back-scattered electron (BSE) image. The compositional change is minute since again no detectable contrast is observed in the image though the topographical contrast is apparent like that in the SE image. Scale bar = 200 μm.

FIGURE 2 in X-ray Microanalysis and the Chemical Elemental Composition of Gorgonian and Pennatulacean Axial Structures (Anthozoa, Octocorallia)

FIGURE 2. Energy dispersive spectrometer (EDS) area scan dataset. (A) EDS site of interest BSE image in a cross-sectional view of a gorgonian Isis hippuris axial skeleton acquired by INCA Energy software using the same region as Figure 1, where spectrum 1 was collected across the full span of the maximum horizontal length of the axial surface and spectrum 2 was collected across the full span of the maximum vertical length of the axial surface. Scale bar = 100 μm. (B) Bar chart of the quantitative results from (C) spectrum 1 for reference in that the analytical results of the two sites are fairly similar as presented in Table 1.