Phase determination in protein x-ray crystallography at low resolution – 6.0 Å Data from rubredoxin via the pseudoatom glob approximation

1999 ◽  
Vol 214 (10) ◽  
Author(s):  
D. L. Dorset ◽  
M. P. McCourt
Keyword(s):  
Phase Error ◽  
Direct Methods ◽  
Basis Set ◽  
X Ray Diffraction ◽  
Screening Criteria ◽  
X Ray ◽  
X Ray Crystallography ◽  
Protein X ◽  
Scattering Factor ◽  
The Fourier Transform

AbstractWith a re-scaled pseudoatom scattering factor approximation to the Fourier transform of globular density units in the protein, the crystal structure of rubredoxin was determined from experimental x-ray diffraction data by direct methods at 6 Å resolution. The Sayre equation expanded a relatively small basis set and screening criteria, such as density flatness and a Patterson correlation coefficient, selected the best of several possible solutions. In the two-dimensional determination, principal peak positions were located in the maps, giving a mean phase error of 57.6° for all 17

Reminiscences and discoveries: Dorothy Hodgkin and the Indian connection

1996 ◽  
Vol 50 (1) ◽  
pp. 115-127 ◽  
Keyword(s):  
Large Angle ◽  
Direct Methods ◽  
Statistical Fluctuation ◽  
Organic Crystals ◽  
X Ray Diffraction ◽  
X Ray ◽  
X Ray Crystallography ◽  
Angle Scattering ◽  
Molecular Sizes ◽  
Indian Institute Of Science

Dorothy Hodgkin - as crystallographer, scientist and human being - far surpasses most, and so it is not easy to write about her many-splendoured personality. Instead, my aim here will he to discuss her influence on the growth of X-ray crystallography in India, directly through those who worked with her and indirectly by her travelling all over this country. In such an account, one must be pardoned for some personal element creeping in. In the twenties, India had developed a fairly strong tradition in X-ray physics. The six-week visit of C.V. Raman to Europe in 1921 greatly changed his research interests. On seeing the blue of the Mediterranean he started his researches on the scattering of light in liquids which finally culminated in the discovery of what is now called the Raman Effect. His encounter with Sir William Bragg and his work on naphthalene structure started three lines of research in India. First, Raman fabricated an X-ray tube and was amongst the earliest to use X-ray diffraction as a structural tool to study liquids. He showed that while in large-angle scattering the haloes reflected specific molecular sizes and packing shapes, small-angle scattering was directly related to the statistical fluctuation of density in a liquid. Second, Raman knew that Bragg’s first structure of naphthalene was not consistent with its birefringence, while the second one was. With this as cue he and his school launched extensive studies on the optical and magnetic anisotropy of organic crystals to get vital information on the arrangements of molecules in the crystalline state. Third, one of his students, Kedareshwar Bannerjee, was amongst the earliest to probe into the problem of phase determination by direct methods and for this he used Bragg’s data on naphthalene. Unfortunately, in spite of this early lead, it was not until 1951 that the first crystal structure was solved in India using Fourier methods by Gopinath Kartha. The Indian Institute of Science (IISc) had great hopes of starting a powerful school of X-ray crystallography when G.N. Ramachandran came back from Cambridge. But he went over to Madras, and there he established one of the most renowned Schools of Biophysics. With Gopinath Kartha he solved the structure of collagen.

Electron exposure-dependent contrast transfer

1978 ◽  
Vol 36 (1) ◽  
pp. 94-95 ◽  
Author(s):  
Wah Chiu ◽  
Robert M. Glaeser
Keyword(s):  
High Resolution ◽  
Phase Error ◽  
Structural Phase ◽  
Image Data ◽  
X Ray ◽  
X Ray Crystallography ◽  
Image Recording ◽  
Replacement Method ◽  
Isomorphous Replacement ◽  
Protein X

The use of electron microscope images for high resolution biological structure analysis has the important advantage that the structural phase information, which is not easily obtained in x-ray or electron diffraction studies, may be easily obtained from images by suitable numerical computations. It has been shown that the phase error determined from image data is much smaller than that which is generally achieved in the use of the isomorphous replacement method in protein x-ray crystallography (1). Due to the constraints imposed by electron radiation damage in the specimen, however, it is quite difficult to obtain high resolution image data for most biological specimens. The use of low-dose image recording techniques, and subsequent computer averaging, has made it possible to obtain 7 Å resolution images of a crystalline specimen embedded in glucose (1). The limitation at this resolution could be caused by instrumental factors and/or poor signal transfer in the recording medium when it is exposed to only a small number of electrons.

Inorganic Crystal Structures Solved from EM Images and Refined to 0.02 À Accuracy Against Electron Diffraction Data

1997 ◽  
Vol 3 (S2) ◽  
pp. 1141-1142
Author(s):  
Sven Hovmöller ◽  
Xiaodong Zou ◽  
Thomas Weirich
Keyword(s):  
Single Crystal ◽  
Organic Molecules ◽  
Direct Methods ◽  
Electron Diffraction Data ◽  
Crystal Data ◽  
Phase Problem ◽  
X Ray Diffraction ◽  
X Ray ◽  
X Ray Crystallography ◽  
Inorganic Crystal

Single crystal X-ray diffraction is the traditional method for accurate crystal structure determination. A major difficulty in X-ray crystallography is the phase problem; diffracted intensities contain amplitude information but no phases. In order to solve a structure, the phases of at least the strongest reflections must be estimated by Patterson techniques, so-called direct methods or in any other way. Once the structure has been solved (i.e. the atoms found to within about 0.2 Ångström of their correct positions), then refinement is rather straight-forward for single crystal data. Typically, single crystals diffract to about 1 Â resolution. After refinement, the atomic co-ordinates are obtained with an accuracy of about 0.01 Â for organic molecules and down to 0.001 Â for inorganic structures. One limitation of single crystal X-ray diffraction is that the crystals need to be at least about 10μm in all dimensions in order to diffract, even if the radiation source is a synchrotron.

Solid state and solution stereochemistry of crown ethers and models. ortho-Dimethoxydiphenyl ether and related dibenzo-15-crown-5 and tetrabenzo-30-crown-10 ethers as studied by X-ray crystallography and 1H and 13C NMR spectroscopy

1994 ◽  
Vol 72 (5) ◽  
pp. 1218-1224 ◽  
Author(s):  
G. W. Buchanan ◽  
A. Rodrigue ◽  
K. Bourque ◽  
A. C. Chiverton ◽  
I. R. Castleden ◽  
...  
Keyword(s):  
Solid Phase ◽  
Direct Methods ◽  
13C Nmr Spectroscopy ◽  
Structural Features ◽  
X Ray Diffraction ◽  
1H And 13C Nmr ◽  
Space Group ◽  
X Ray ◽  
X Ray Crystallography ◽  
C Nmr

Solid phase 45.3 MHz 13C NMR spectra of ortho-dimethoxydiphenyl ether, 1, dibenzo[b,e]-15-crown-5- ether, 2, and tetrabenzo[b,e,q,t]-30-crown-10 ether, 3, have been obtained. Chemical shift trends are discussed in terms of the asymmetric units and structural features available from X-ray crystallographic data. Comparison with solution 13C spectra are made. The crystal structures of 1 and 3 were determined by X-ray diffraction at room temperature. 1 crystallizes in space group P21/a with a = 13.366(1), b = 8.230(1), c = 12.303(1) Å, β = 116.63(1)°, Z = 4. 3 crystallizes in space group P21/c with a = 7.903(1), b = 26.337(2), c = 7.852(1) Å, β = 97.28(1)°, Z = 2. The structures were solved by direct methods and refined by full-matrix least squares to residuals of 0.055 using 1727 reflections for 1 and of 0.042 using 2590 reflections for 3.

Initial elemental analysis by X-ray crystallography

2011 ◽  
Vol 44 (3) ◽  
pp. 625-627 ◽  
Author(s):  
Jianglin Feng
Keyword(s):  
Chemical Composition ◽  
Elemental Analysis ◽  
X Ray Diffraction ◽  
Fourier Synthesis ◽  
X Ray ◽  
X Ray Crystallography ◽  
Structure Factors ◽  
Isotropic Displacement Parameter ◽  
Initial Identification ◽  
Scattering Factor

A method is proposed for the initial identification of non-hydrogen atomic species in a crystal from X-ray diffraction intensities when the chemical composition is not available. When atom positions are determined, a portion of the scattering factor curve for each atom can be obtained by Fourier synthesis with reflections from concentric shells. From these curves, the atomic number and the isotropic displacement parameter for all non-H atoms, and the scaling constant of the structure factors, can be approximately determined.

Crystal structure determination of the conformation of two bicyclo[3.3.1]nonan-ones

1985 ◽  
Vol 63 (6) ◽  
pp. 1166-1169 ◽  
Author(s):  
John F. Richardson ◽  
Ted S. Sorensen
Keyword(s):  
Crystal Structure ◽  
Direct Methods ◽  
Chair Conformation ◽  
Molecular Structures ◽  
Boat Conformation ◽  
X Ray Diffraction ◽  
Space Group ◽  
X Ray ◽  
Final Agreement

The molecular structures of exo-7-methylbicyclo[3.3.1]nonan-3-one, 3, and the endo-7-methyl isomer, 4, have been determined using X-ray-diffraction techniques. Compound 3 crystallizes in the space group [Formula: see text] with a = 15.115(1), c = 7.677(2) Å, and Z = 8 while 4 crystallizes in the space group P21 with a = 6.446(1), b = 7.831(1), c = 8.414(2) Å, β = 94.42(2)°, and Z = 2. The structures were solved by direct methods and refined to final agreement factors of R = 0.041 and R = 0.034 for 3 and 4 respectively. Compound 3 exists in a chair–chair conformation and there is no significant flattening of the chair rings. However, in 4, the non-ketone ring is forced into a boat conformation. These results are significant in interpreting what conformations may be present in the related sp2-hybridized carbocations.

Configurational and conformational studies on condensation products of biogenic amines with 2,5-anhydro-D-mannose

1985 ◽  
Vol 63 (11) ◽  
pp. 2915-2921 ◽  
Author(s):  
Ian M. Piper ◽  
David B. MacLean ◽  
Romolo Faggiani ◽  
Colin J. L. Lock ◽  
Walter A. Szarek
Keyword(s):  
Hydrogen Bond ◽  
Intermolecular Hydrogen Bond ◽  
Direct Methods ◽  
Conformational Studies ◽  
X Ray ◽  
X Ray Crystallography ◽  
H Nmr ◽  
Twist Conformation ◽  
Cell Dimensions ◽  
Internal Hydrogen Bond

The products of a Pictet–Spengler condensation of tryptamine and of histamine with 2,5-anhydro-D-mannose have been studied by X-ray crystallography to establish their absolute configuration. 1(S)-(α-D-Arabinofuranosyl)-1,2,3,4-tetrahydro-β-carboline (1), C16H20N20O4, is monoclinic, P21 (No. 4), with cell dimensions a = 13.091(4), b = 5.365(1), c = 11.323(3) Å, β = 115.78(2)°, and Z = 2. 4-(α-D-Arabinofuranosyl)imidazo[4,5-c]-4,5,6,7-tetrahydropyridine (3), C11H17N3O4, is orthorhombic, P212121 (No. 19), with cell dimensions a = 8.118(2), b = 13.715(4), c = 10.963(3) Å, and Z = 4. The structures were determined by direct methods and refined to R1 = 0.0514, R2 = 0.0642 for 3210 reflections in the case of 1, and to R1 = 0.0312, R2 = 0.0335 for 1569 reflections in the case of 3. Bond lengths and angles within both molecules are normal and agree well with those observed in related structures. In 3 the base and sugar adopt a syn arrangement, which is maintained by an internal hydrogen bond between O(2′) and N(3). The sugar adopts a normal 2T3 twist conformation. The sugar has the opposite anti arrangement in the β-carboline 1 and the conformation of the sugar is unusual; it is close to an envelope conformation with O(4′) being the atom out of the plane. This conformation is caused by a strong intermolecular hydrogen bond from O(5′) in a symmetry-related molecule to O(4′). Both compounds are held together in the crystal by extensive hydrogen-bonding networks. The conformations of the compounds in solution have been investigated by 1H nmr spectroscopy, and the results obtained were compared with those obtained by X-ray crystallography for 1 and 3.

Synthesis and characterization of a linked, π-π stacked organotin compound of 2-mercapto-6-nitrobenzothiazolyl diphenyltin chloride with 2-ethoxyl-6-nitrobenzothiazole

2003 ◽  
Vol 81 (7) ◽  
pp. 825-831 ◽  
Author(s):  
Chunlin Ma ◽  
Qin Jiang ◽  
Rufen Zhang
Keyword(s):  
Title Compound ◽  
Organotin Compound ◽  
X Ray Diffraction ◽  
X Ray ◽  
Stacking Interaction ◽  
X Ray Crystallography ◽  
H Nmr ◽  
Π Stacking ◽  
Π Stacking Interaction ◽  
Molecular Components

The new organotin compound, Ph2Sn(Cl)[S(C7H3N2O2S)]·[(C7H3N2O2S)OEt], assembled by an intermolecular aromatic benzothiazole–benzothiazole π-π stacking interaction, has been synthesized by the reaction of diphenyltin dichloride with 2-mercapto-6-nitrobenzothiazole. The title compound was characterized by elemental, IR, 1H NMR, and X-ray crystallography analyses. Single-crystal X-ray diffraction data reveals that the title compound has two different molecular components. The component Ph2Sn(Cl)[S(C7H3N2O2S)] has a pentacoordinate tin, which further forms an infinite one-dimensional chain by intermolecular non-bonded Cl···S interactions, resulting in an intercalation lattice that holds (C7H3N2O2S)OEt molecules. The formation of the molecule (C7H3N2O2S)OEt as well as its intercalated mechanism has also been discussed.Key words: organotin, assemble, π-π stacking interaction, 2-mercapto-6-nitrobenzothiazole, non-bonded interaction, crystal structure.

scholarly journals Observation of ordered organic capping ligands on semiconducting quantum dots via powder X-ray diffraction

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Jason J. Calvin ◽  
Tierni M. Kaufman ◽  
Adam B. Sedlak ◽  
Michelle F. Crook ◽  
A. Paul Alivisatos
Keyword(s):  
Quantum Dots ◽  
Colloidal System ◽  
X Ray Diffraction ◽  
X Ray ◽  
Ligand Shell ◽  
Scattering Factor ◽  
Organic Capping ◽  
Capping Ligands ◽  
Key Techniques ◽  
Inorganic Structure

AbstractPowder X-ray diffraction is one of the key techniques used to characterize the inorganic structure of colloidal nanocrystals. The comparatively low scattering factor of nuclei of the organic capping ligands and their propensity to be disordered has led investigators to typically consider them effectively invisible to this technique. In this report, we demonstrate that a commonly observed powder X-ray diffraction peak around $$q=1.4{\AA}^{-1}$$ q = 1.4 Å − 1 observed in many small, colloidal quantum dots can be assigned to well-ordered aliphatic ligands bound to and capping the nanocrystals. This conclusion differs from a variety of explanations ascribed by previous sources, the majority of which propose an excess of organic material. Additionally, we demonstrate that the observed ligand peak is a sensitive probe of ligand shell ordering. Changes as a function of ligand length, geometry, and temperature can all be readily observed by X-ray diffraction and manipulated to achieve desired outcomes for the final colloidal system.

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