X-Ray analysis of bovine pancreatic ribonuclease analogs: A difference Fourier at 2.8 Å resolution of (O r n10)-ribonuclease S′

Biopolymers ◽  
1977 ◽  
Vol 16 (6) ◽  
pp. 1371-1376 ◽  
Author(s):  
G. Valle ◽  
G. Zanotti ◽  
B. Filippi ◽  
A. Del Pra
Keyword(s):  
Pancreatic Ribonuclease ◽  
X Ray ◽  
Difference Fourier

Difference Fourier Analysis of Glucose Embedded and Frozen Hydrated Purple Membrane

1982 ◽  
Vol 40 ◽  
pp. 74-75
Author(s):  
Jules S. Jaffe ◽  
Robert M. Glaeser
Keyword(s):  
Purple Membrane ◽  
Data Set ◽  
High Resolution Data ◽  
X Ray ◽  
X Ray Crystallography ◽  
Fourier Techniques ◽  
Versus Protein ◽  
The Difference ◽  
Difference Fourier ◽  
Ideal Method

Although difference Fourier techniques are standard in X-ray crystallography it has only been very recently that electron crystallographers have been able to take advantage of this method. We have combined a high resolution data set for frozen glucose embedded Purple Membrane (PM) with a data set collected from PM prepared in the frozen hydrated state in order to visualize any differences in structure due to the different methods of preparation. The increased contrast between protein-ice versus protein-glucose may prove to be an advantage of the frozen hydrated technique for visualizing those parts of bacteriorhodopsin that are embedded in glucose. In addition, surface groups of the protein may be disordered in glucose and ordered in the frozen state. The sensitivity of the difference Fourier technique to small changes in structure provides an ideal method for testing this hypothesis.

Manganese behavior in hydroxyapatite crystals revealed by X-ray difference Fourier maps

2020 ◽  
Vol 46 (8) ◽  
pp. 10585-10597
Author(s):  
P.H. Oliveira ◽  
L.A.B. Santana ◽  
N.S. Ferreira ◽  
S. Sharifi-Asl ◽  
T. Shokuhfar ◽  
...  
Keyword(s):  
X Ray ◽  
Difference Fourier ◽  
Hydroxyapatite Crystals

Use of CrKα radiation to enhance the signal from anomalous scatterers including sulfur

2000 ◽  
Vol 33 (3) ◽  
pp. 876-881 ◽  
Author(s):  
Witek Kwiatkowski ◽  
Joseph P. Noel ◽  
Senyon Choe
Keyword(s):  
Disulfide Bonds ◽  
Diffraction Method ◽  
Protein Molecule ◽  
Test Case ◽  
Data Sets ◽  
X Ray ◽  
Multi Wavelength ◽  
Anomalous Signal ◽  
Difference Fourier ◽  
Hiv 1

The anomalous signals from scatterers such as sulfur (S) and arsenic (As) were compared in diffraction data sets collected from an X-ray source with three different targets, Au, Cu and Cr, on a multi-target rotating anode. HIV-1 integrase crystals served as the test case for this study. The crystalline specimen of HIV-1 integrase contains in each protein molecule two As atoms, each covalently bound to a cysteine S atom, and two additional S atoms derived from methionine. It was found that the CrKα radiation gave the clearest peaks in anomalous difference Fourier maps, although the signal-to-noise ratios of the anomalous signal for the CuKα and CrKα data were similar but better than that for AuLα. This result was in spite of the fourfold higher flux from the Cu anodeversusthe Cr anode. For all three X-ray wavelengths, anomalous difference Fourier maps calculated with bias-removed phases derived from the known atomic model revealed clear peaks at the two As sites. However, only in the map calculated using the CrKα data were both peaks of the expected ellipsoidal shape, enveloping the As atom and the adjacent S atom. None of the S sites was apparent in difference maps calculated using the AuLα data. The ability to enhance the S-derived anomalous signal using CrKα radiation has particularly useful applications in the structure determination of proteins, for example in resolving ambiguities in the chain tracing of a protein with numerous disulfide bonds and in assigning amino acid identities. Additionally, anomalous difference Patterson maps calculated from the CrKα data were sufficiently clear to identify the As-related peaks. These results form the groundwork for in-house phase determination with the multi-wavelength anomalous diffraction method.

scholarly journals X-ray diffraction studies of two dimeric variants of human pancreatic ribonuclease

2008 ◽  
Vol 64 (a1) ◽  
pp. C356-C356
Author(s):  
F. Sica ◽  
A. Merlino ◽  
E. Pizzo ◽  
R. Piccoli ◽  
G. D'Alessio ◽  
...  
Keyword(s):  
X Ray Diffraction ◽  
Pancreatic Ribonuclease ◽  
X Ray ◽  
Human Pancreatic Ribonuclease

Carbon incorporation in plumbogummite-group minerals

2011 ◽  
Vol 75 (1) ◽  
pp. 145-158 ◽  
Author(s):  
I. E. Grey ◽  
F. L. Shanks ◽  
N. C. Wilson ◽  
W. G. Mumme ◽  
W. D. Birch
Keyword(s):  
Organic Carbon ◽  
Rietveld Analysis ◽  
Chemical Analyses ◽  
X Ray Diffraction ◽  
Carbon Incorporation ◽  
X Ray ◽  
Wet Chemical ◽  
Difference Fourier ◽  
Large Contraction ◽  
Direct Confirmation

AbstractNon-stoichiometric, carbon-containing crandallite from Guatemala and plumbogummite from Cumbria have been characterized using electron microprobe (EMPA) and wet-chemical analyses, Rietveld analysis of powder X-ray diffraction (PXRD) patterns, and infrared (IR), Raman and cathodoluminescence (CL) spectroscopies. The samples contain 11.0 and 4.8 wt.% CO2, respectively. The IR spectra for both samples show a doublet in the range 1410–1470 cm–1, corresponding to CO3 vibrations. Direct confirmation of CO3 replacing PO4 was obtained from difference Fourier maps in the Rietveld analysis. Carbonate accounts for 67% of the C in the plumbogummite and 20% of the C in the Guatemalan crandallite, the remainder being present as nano-scale organic carbon. The CO3 substitution for PO4 is manifested in a large contraction of the tetrahedral volume (14–19%) and by a contraction of the a axis, analogous to observations for carbonate-containing fluorapatites. Stoichiometric crandallite from Utah was characterized using the same methods, for comparison with the non-stoichiometric, carbon-bearing phases.

RuII–hydride–tropcomplexes: X-ray single-crystal determination and quantum-chemical calculations

2013 ◽  
Vol 69 (12) ◽  
pp. 1421-1426 ◽  
Author(s):  
Gustavo Santiso-Quinones ◽  
Rafael Rodriguez-Lugo ◽  
Vittorio Sacchetti ◽  
Hansjörg Grützmacher
Keyword(s):  
Quantum Chemical Calculations ◽  
Quantum Chemical ◽  
Theoretical Calculations ◽  
Data Sets ◽  
Space Group ◽  
X Ray ◽  
H Nmr ◽  
Axial Ligands ◽  
Catalytically Active ◽  
Difference Fourier

As part of our search for catalytically active RuII–hydride complexes, we have synthesized and crystallographically characterized three different ruthenium species, namely dihydrido[(SR)-(10,11-η)-N-(pyridin-2-ylmethyl-κN)-5H-dibenzo[a,d]cyclohepten-5-amine](triphenylphosphane-κP)ruthenium(II) tetrahydrofuran monosolvate, [RuH2(C21H18N2)(C18H15P)]·C4H8O or (SR)-[RuII(H)2{N-(pyridin-2-ylmethyl)tropNH}(PPh3)]·THF, (1), chlorido{(1SR,2RS)-N,N′-bis[(10,11-η)-5H-dibenzo[a,d]cyclohepten-5-amine]ethane-1,2-diamine-κ2N,N′}hydridoruthenium(II) dimethoxyethane hemisolvate, [RuClH(C32H28N2)]·0.5C4H10O2or (1SR,2RS)-[RuII(H)(Cl){tropNH(CH2)2HNtrop}]·DME, (2), and chlorido{(1SR,2RS)-N,N′-bis[(10,11-η)-5H-dibenzo[a,d]cyclohepten-5-amine]propane-1,3-diamine-κ2N,N′}hydridoruthenium(II), [RuClH(C33H30N2)] or (1SR,2RS)-[RuII(H)(Cl){tropNH(CH2)3HNtrop}], (3), wheretropis 5H-dibenzo[a,d]cycloheptene. In all three complexes, the RuIIcenter resides in an octahedral coordination environment. For (1)–(3), the hydride atoms were located in a difference Fourier map and were refined freely. In solution, the1H NMR spectra of all species show the presence of the hydride resonance. Comparison with quantum-chemical calculations reveals that the crystallographic data sets are plausible. In every case, the prediction is in very good agreement with the observed X-ray data. Not only the observed geometry is predicted well but also the Ru—H(hydride) bond lengths are reproduced remarkably well. Complexes (1) and (2) crystallized in the triclinicP\overline{1} space group, while (3) crystallized in the tetragonal space groupI41/a. For (3), there is disorder of the axial ligands producing two isomers (in a 98.7:1.3 ratio). Details of the synthesis, characterization, X-ray analysis, and theoretical calculations for complexes (1)–(3) are presented.

Gemmological investigation of a synthetic blue beryl: a multi-methodological study

2008 ◽  
Vol 72 (3) ◽  
pp. 799-808 ◽  
Author(s):  
I. Adamo ◽  
G. D. Gatta ◽  
N. Rotiroti ◽  
V. Diella ◽  
A. Pavese
Keyword(s):  
Crystal Structure ◽  
Inductively Coupled Plasma ◽  
Tetrahedral Site ◽  
X Ray Diffraction ◽  
Thermo Gravimetric ◽  
X Ray ◽  
Cell Parameters ◽  
Inductively Coupled ◽  
The Difference ◽  
Difference Fourier

AbstractA multi-methodological investigation of a synthetic Cu/Fe-bearing blue beryl [IV(Be2.86Cu0.14)∑=3.00VI(Al1.83Fe3+0.14Mn2+0.03Mg0.03)∑=2.03IV(Si5.97Al0.03∑=6.00O18.(Li0.12Na0.04.0.40H2O)] has been performed by means of gemmological standard testing, electron microprobe chemical analyses, laser ablation inductively coupled plasma mass spectroscopy, thermo-gravimetric analyses, infrared spectroscopy and single-crystal X-ray diffraction in order to determine the gemmological properties, crystal structure and crystal-chemistry of this material. The increasing production of marketable hydrothermal synthetic beryls with 'exotic' colours and the small number of studies on the accurate location of chromophores in the crystal structure inspired this multi-methodological investigation. The X-ray structural refinements confirm that the space group of the Cu/Fe-bearing blue beryl is P6/mcc, with unit-cell parameters: 9.2483 ≤ a ≤ 9.2502 Å and 9.2184 ≤ c ≤ 9.2211 Å. The analysis of the difference Fourier maps of the electron density suggests that Cu is located at the tetrahedral site (Wyckoff 6fposition) along with Be, whereas Fe shares the octahedral site with Al (4c position). No evidence of extra-framework Cu/Fe-sites (i.e. channel sites) has been found. The Li is probably located at the extra-framework 2b site. Infrared spectra show that the H2O molecules are present with two configurations: one with the H···H vector oriented ‖[0001] and the other with H···H vector oriented ⊥[0001].

A crystallographic and spectroscopic study on the imine-amine tautomerism of 2-hydroxyaldimine compounds

2006 ◽  
Vol 221 (10) ◽  
Author(s):  
Hasan Nazir ◽  
Cengiz Arici ◽  
Kaan C. Emregül ◽  
Orhan Atakol
Keyword(s):  
Molecular Structure ◽  
Spectroscopic Study ◽  
Schiff Bases ◽  
Ftir Spectra ◽  
Molecular Structures ◽  
X Ray Diffraction ◽  
X Ray ◽  
The Difference ◽  
Difference Fourier

AbstractThe molecular structures of N-(2-hydroxy ethyl)-3,5-dinitrosalicylaldimine and N-N′-bis(acetophe-nylketimine)-1,4-diaminobuthane were determined using X-ray diffraction. It was established using the difference Fourier map that the phenolic hydrogens were situated on the iminic nitrogen. Identical observations of the molecular structure were made for similar Schiff bases in literature, and it was established that this situation was not in agreement with the IR and NMR results. The molecular structure of N-(4-hydroxylphenyl)-benzaldimine was determined using X-ray diffraction for comparison. Similar compounds were prepared and their FTIR spectra were investigated.

scholarly journals Crystallographic studies on Mn atoms in Photosystem II using K-edge wavelength

2014 ◽  
Vol 70 (a1) ◽  
pp. C350-C350
Author(s):  
Yasufumi Umena ◽  
Keisuke Kawakami ◽  
Jian-Ren Shen ◽  
Nobuo Kamiya
Keyword(s):  
Photosystem Ii ◽  
Molecular Oxygen ◽  
Electronic State ◽  
Absorption Edge ◽  
Water Oxidation ◽  
Catalytic Mechanism ◽  
Anomalous Scattering ◽  
Oxygen Evolving Complex ◽  
X Ray ◽  
Difference Fourier

Molecular oxygen on Earth is generated from photosynthesis by cyanobacteria, algae and plants, where water molecules are split by Photosystem II (PSII). PSII catalyzes light-induced water oxidation leading to the production of protons, electrons and molecular oxygen. The catalytic center of oxygen evolving complex (OEC) in PSII is composed of four Mn atoms and one Ca atom organized in a Mn4CaO5-cluster, which cycles through several different redox states to accomplish the catalytic process. Cyanobacterial PSII is a multi-subunits membrane protein complex composed of 17 membrane-spanning subunits, 3 membrane-extrinsic subunits and about 80 co-factor molecules with a total molecular weight of 350 kDa as a monomer. We reported the PSII structure at 1.9 Å resolution prepared from Thermosynechococcus vulcanus (PDB code: 3ARC)[1]. We determined unambiguously the positions of the atoms in OEC using the electron density map corresponding to each of five metal atoms and five oxygen atoms, for the first time. However, the valences of each of the four Mn atoms and their participation in the redox reactions in OEC are not fully understood. In order to uncover the catalytic mechanism of light-induced water oxidation by OEC, it is important to determine the valence of each Mn atom as well as to solve the detailed structure. In this study, we analyze the electronic state of each Mn atom in OEC by X-ray crystallographic analysis using Mn K-absorption edge wavelength. The Mn K-absorption edge depends on the oxidation number, and the anomalous scattering factor changes greatly for the Mn atoms in different oxidation states. We collected the anomalous difference data from PSII crystals using the wavelength (~1.8921 Å) on the Mn K-absorption edge at beamline BL38B1 and BL41XU of SPring-8 in Japan. The calculated anomalous difference Fourier map indicated different intensities among the four Mn atoms in OEC. This may suggest the different electronic state among the four Mn atoms in OEC. However, there is a possibility that these Mn atoms are reduced by X-ray exposures to some extent, and so the valences of these Mn atoms were not determined completely. We will discuss the relationship between peak heights of the anomalous difference Fourier map and the valence among the four Mn atoms in OEC.

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