X-ray data processing

The method of molecular structure determination by X-ray crystallography is a little over a century old. The history is described briefly, along with developments in X-ray sources and detectors. The fundamental processes involved in measuring diffraction patterns on area detectors, i.e. autoindexing, refining crystal and detector parameters, integrating the reflections themselves and putting the resultant measurements on to a common scale are discussed, with particular reference to the most commonly used software in the field.

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Structure of catalase determined by MicroED

eLife ◽

10.7554/elife.03600 ◽

2014 ◽

Vol 3 ◽

Cited By ~ 75

Author(s):

Brent L Nannenga ◽

Dan Shi ◽

Johan Hattne ◽

Francis E Reyes ◽

Tamir Gonen

Keyword(s):

Structure Determination ◽

Three Dimensional ◽

Bovine Liver ◽

Electron Crystallography ◽

X Ray ◽

X Ray Crystallography ◽

Continuous Rotation ◽

Bovine Liver Catalase ◽

Diffraction Patterns ◽

Atomic Analysis

MicroED is a recently developed method that uses electron diffraction for structure determination from very small three-dimensional crystals of biological material. Previously we used a series of still diffraction patterns to determine the structure of lysozyme at 2.9 Å resolution with MicroED (<xref ref-type="bibr" rid="bib26">Shi et al., 2013</xref>). Here we present the structure of bovine liver catalase determined from a single crystal at 3.2 Å resolution by MicroED. The data were collected by continuous rotation of the sample under constant exposure and were processed and refined using standard programs for X-ray crystallography. The ability of MicroED to determine the structure of bovine liver catalase, a protein that has long resisted atomic analysis by traditional electron crystallography, demonstrates the potential of this method for structure determination.

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N,N′-Dialkyl-4-Aryl-3,4-Dihydropyrimidinones and Thiones: Ceric Ammonium Nitrate Catalyzed Synthesis and Molecular Structure Determination by X-ray Crystallography

Journal of Heterocyclic Chemistry ◽

10.1002/jhet.2735 ◽

2016 ◽

Vol 54 (2) ◽

pp. 1486-1491 ◽

Cited By ~ 1

Author(s):

Chingrishon Kathing ◽

Sushil Kumar ◽

Shokip Tumtin ◽

Nongthombam Geetmani Singh ◽

Jims World Star Rani ◽

...

Keyword(s):

Molecular Structure ◽

Ammonium Nitrate ◽

Structure Determination ◽

Ceric Ammonium Nitrate ◽

X Ray ◽

X Ray Crystallography

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Image Processing and Lattice Determination for Three-Dimensional Nanocrystals

Microscopy and Microanalysis ◽

10.1017/s1431927611012244 ◽

2011 ◽

Vol 17 (6) ◽

pp. 879-885 ◽

Cited By ~ 8

Author(s):

Linhua Jiang ◽

Dilyana Georgieva ◽

Igor Nederlof ◽

Zunfeng Liu ◽

Jan Pieter Abrahams

Keyword(s):

Molecular Structure ◽

Three Dimensional ◽

X Ray ◽

X Ray Crystallography ◽

Hard Materials ◽

Cryo Electron Microscopy ◽

Diffraction Patterns ◽

Radiation Hard ◽

Orientation Parameters

AbstractThree-dimensional nanocrystals can be studied by electron diffraction using transmission cryo-electron microscopy. For molecular structure determination of proteins, such nanosized crystalline samples are out of reach for traditional single-crystal X-ray crystallography. For the study of materials that are not sensitive to the electron beam, software has been developed for determining the crystal lattice and orientation parameters. These methods require radiation-hard materials that survive careful orienting of the crystals and measuring diffraction of one and the same crystal from different, but known directions. However, as such methods can only deal with well-oriented crystalline samples, a problem exists for three-dimensional (3D) crystals of proteins and other radiation sensitive materials that do not survive careful rotational alignment in the electron microscope. Here, we discuss our newly released software AMP that can deal with nonoriented diffraction patterns, and we discuss the progress of our new preprocessing program that uses autocorrelation patterns of diffraction images for lattice determination and indexing of 3D nanocrystals.

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From Penicillin to the Ribosome: Revolutions in the Determination and Use of Molecular Structure in Chemistry and Biology

Australian Journal of Chemistry ◽

10.1071/ch04090 ◽

2004 ◽

Vol 57 (9) ◽

pp. 829 ◽

Cited By ~ 2

Author(s):

Edward N. Baker

Keyword(s):

Biological Sciences ◽

Molecular Structure ◽

Structural Genomics ◽

Structure Determination ◽

Biological Function ◽

Structural Information ◽

Structure Based Drug Design ◽

X Ray ◽

X Ray Crystallography

A revolution in structural analysis is in progress in the biological sciences that parallels a similar revolution that took place in chemistry 40–50 years ago. This has major implications for chemistry, offering exciting opportunities at the interface between chemistry and biology. The advances are driven by the value of structural information in biology, for understanding biological function, and for applications in structure-based drug design and structural genomics. Two directions are apparent: towards technically challenging biological structures and assemblies, typified by the potassium channel and the ribosome; and towards high-throughput structure determination of many, smaller, proteins, as in structural genomics. In this review, the advances in molecular biology and in structure determination by X-ray crystallography that make these developments possible are discussed, together with appropriate examples.

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Faculty Opinions recommendation of Comparisons of NMR spectral quality and success in crystallization demonstrate that NMR and X-ray crystallography are complementary methods for small protein structure determination.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1029453.344422 ◽

2005 ◽

Author(s):

Deyou Zheng

Keyword(s):

Protein Structure ◽

Structure Determination ◽

Protein Structure Determination ◽

Spectral Quality ◽

Small Protein ◽

X Ray ◽

Complementary Methods ◽

X Ray Crystallography

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Molekül- und Kristallstruktur von 1.1-Dimethylsilylentitanocendichlorid, (CH3)2Si(C5H4)2TiCl2 / Molecular and Crystal Structure of l,r-Dimethylsilylene Titanocene Dichloride, (CH3)2Si(C5H4)2TiCl2

Zeitschrift für Naturforschung B ◽

10.1515/znb-1981-1002 ◽

1981 ◽

Vol 36 (10) ◽

pp. 1208-1210 ◽

Cited By ~ 12

Author(s):

Hartmut Köpf ◽

Joachim Pickardt

Keyword(s):

Molecular Structure ◽

Crystal Structure ◽

Structure Determination ◽

Titanocene Dichloride ◽

Molecular And Crystal Structure ◽

Monoclinic Space Group ◽

Crystal Data ◽

Space Group ◽

X Ray ◽

Structural Dimensions

Abstract The molecular structure of the bridged [1]-titanocenophane 1,1'-dimethylsilylene titanocene dichloride, (CH3)2Si(C5H4)2TiCl2, has been investigated by an X-ray structure determination. Crystal data: monoclinic, space group C2/c, Z = 4, a = 1332.9(3), 6 = 988.7(3), c = 1068.9(3) pm, β = 113.43(2)°. The results are compared with the structural dimensions of similar compounds: 1,1'-methylene titanocene dichloride, CH2(C5H4)TiCl2, with the unbridged titanocene dichloride, (C5H5)2TiCl2 and the ethylene-bridged compound (CH2)2(C5H4)2TiCl2

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Structural Characterization of Heterodinuclear ZnII-LnIII Complexes (Ln = Pr, Nd) with a Ring-Contracted H2valdien-Derived Schiff Base Ligand

Journal of Chemical Crystallography ◽

10.1007/s10870-021-00891-4 ◽

2021 ◽

Author(s):

Shabana Noor ◽

Richard Goddard ◽

Fehmeeda Khatoon ◽

Sarvendra Kumar ◽

Rüdiger W. Seidel

Keyword(s):

Molecular Structure ◽

Schiff Base ◽

Structural Characterization ◽

Schiff Base Ligand ◽

Crystal And Molecular Structure ◽

X Ray ◽

X Ray Crystallography ◽

Imidazoline Ring

AbstractSynthesis and structural characterization of two heterodinuclear ZnII-LnIII complexes with the formula [ZnLn(HL)(µ-OAc)(NO3)2(H2O)x(MeOH)1-x]NO3 · n H2O · n MeOH [Ln = Pr (1), Nd (2)] and the crystal and molecular structure of [ZnNd(HL)(µ-OAc)(NO3)2(H2O)] [ZnNd(HL)(OAc)(NO3)2(H2O)](NO3)2 · n H2O · n MeOH (3) are reported. The asymmetrical compartmental ligand (E)-2-(1-(2-((2-hydroxy-3-methoxybenzylidene)amino)-ethyl)imidazolidin-2-yl)-6-methoxyphenol (H2L) is formed from N1,N3-bis(3-methoxysalicylidene)diethylenetriamine (H2valdien) through intramolecular aminal formation, resulting in a peripheral imidazoline ring. The structures of 1–3 were revealed by X-ray crystallography. The smaller ZnII ion occupies the inner N2O2 compartment of the ligand, whereas the larger and more oxophilic LnIII ions are found in the outer O2O2’ site. Graphic Abstract Synthesis and structural characterization of two heterodinuclear ZnII-LnIII complexes (Ln = Pr, Nd) bearing an asymmetrical compartmental ligand formed in situ from N1,N3-bis(3-methoxysalicylidene)diethylenetriamine (H2valdien) through intramolecular aminal formation are reported.

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