Molecular Replacement Method

Argos, Patrick; Rossman, Michael G.

doi:10.1007/978-1-4613-2979-4_10

Cited by 10 publications

(8 citation statements)

References 116 publications

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“…As the structures get larger and more complex, however, this simple trial-and-error method becomes more difficult owing to the exponential growth in the number of interatomic vectors in three dimensions. Over the years many more powerful phasing methods have been developed, including direct methods (44), isomorphous replacements (45), molecular replacement (46), multiple anomalous dispersion (47,48), and solvent flattening (49). The use of other experimental measured phase information, such as noncrystallographic symmetry (50,51), molecular envelope (52) or triplet phases (53,54), can also be exploited to solve protein crystal structures and is of current research interest.…”

Section: The Oversampling Methods and Iterative Algorithms The Phase Pmentioning

confidence: 99%

Extending X-Ray Crystallography to Allow the Imaging of Noncrystalline Materials, Cells, and Single Protein Complexes

Miao

Ishikawa²,

Shen³

et al. 2008

Annu. Rev. Phys. Chem.

233

163

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In 1999, researchers extended X-ray crystallography to allow the imaging of noncrystalline specimens by measuring the X-ray diffraction pattern of a noncrystalline specimen and then directly phasing it using the oversampling method with iterative algorithms. Since then, the field has evolved moving in three important directions. The first is the 3D structural determination of noncrystalline materials, which includes the localization of the defects and strain field inside nanocrystals, and quantitative 3D imaging of disordered materials such as nanoparticles and biomaterials. The second is the 3D imaging of frozen-hydrated whole cells at a resolution of 10 nm or better. A main thrust is to localize specific multiprotein complexes inside cells. The third is the potential of imaging single large protein complexes using extremely intense and ultrashort X-ray pulses. In this article, we review the principles of this methodology, summarize recent developments in each of the three directions, and illustrate a few examples.

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Section: The Oversampling Methods and Iterative Algorithms The Phase Pmentioning

confidence: 99%

Extending X-Ray Crystallography to Allow the Imaging of Noncrystalline Materials, Cells, and Single Protein Complexes

Miao

Ishikawa²,

Shen³

et al. 2008

Annu. Rev. Phys. Chem.

233

163

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show abstract

“…This remarkable achievement is partially attributed to the availability of powerful phase determination techniques such as the direct methods [54], isomorphous replacement [55], multiple wavelength anomalous dispersion (MAD) [28,29] and molecular replacement [26]. However, when a crystal becomes very small or only has one unit cell (i.e.…”

Section: Phase Determination By the Oversampling Methodsmentioning

confidence: 99%

“…Molecular replacement [26] has been used for phasing the SFX data [25,27]. So far, no de-novo phasing has been demonstrated.…”

Section: Serial Femtosecond Crystallographymentioning

confidence: 99%

Emerging opportunities in structural biology with X-ray free-electron lasers

Schlichting

Miao

2012

Current Opinion in Structural Biology

122

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X-ray free-electron lasers (X-FELs) produce X-ray pulses with extremely brilliant peak intensity and ultrashort pulse duration. It has been proposed that radiation damage can be “outrun” by using an ultra intense and short X-FEL pulse that passes a biological sample before the onset of significant radiation damage. The concept of “diffraction-before-destruction” has been demonstrated recently at the Linac Coherent Light Source, the first operational hard X-ray FEL, for protein nanocrystals and giant virus particles. The continuous diffraction patterns from single particles allow solving the classical “phase problem” by the oversampling method with iterative algorithms. If enough data are collected from many identical copies of a (biological) particle, its three-dimensional structure can be reconstructed. We review the current status and future prospects of serial femtosecond crystallography (SFX) and single-particle coherent diffraction imaging (CDI) with X-FELs.

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“…Although we have only implemented the amplitude extension constraint here, we note that there are a few more constraints that can be computed at low resolution to assist the high resolution reconstruction. These constraints include but are not limited to: phase extension 37 , histogram matching 38 , and molecular replacement 39 . Our preliminary simulations to date indicate that enforcing these constraints for large system sizes dramatically improves the reconstruction convergence and will be the subject of subsequent publications.…”

Section: Amplitude Extensionmentioning

confidence: 99%

Three-dimensional structure determination from a single view

Raines

Salha

Sandberg

et al. 2009

Nature

165

112

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The ability to determine the structure of matter in three dimensions has profoundly advanced our understanding of nature. Traditionally, the most widely used schemes for three-dimensional (3D) structure determination of an object are implemented by acquiring multiple measurements over various sample orientations, as in the case of crystallography and tomography, or by scanning a series of thin sections through the sample, as in confocal microscopy. Here we present a 3D imaging modality, termed ankylography (derived from the Greek words ankylos meaning 'curved' and graphein meaning 'writing'), which under certain circumstances enables complete 3D structure determination from a single exposure using a monochromatic incident beam. We demonstrate that when the diffraction pattern of a finite object is sampled at a sufficiently fine scale on the Ewald sphere, the 3D structure of the object is in principle determined by the 2D spherical pattern. We confirm the theoretical analysis by performing 3D numerical reconstructions of a sodium silicate glass structure at 2 A resolution, and a single poliovirus at 2-3 nm resolution, from 2D spherical diffraction patterns alone. Using diffraction data from a soft X-ray laser, we also provide a preliminary demonstration that ankylography is experimentally feasible by obtaining a 3D image of a test object from a single 2D diffraction pattern. With further development, this approach of obtaining complete 3D structure information from a single view could find broad applications in the physical and life sciences.

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Molecular Replacement Method

Cited by 10 publications

References 116 publications

Extending X-Ray Crystallography to Allow the Imaging of Noncrystalline Materials, Cells, and Single Protein Complexes

Extending X-Ray Crystallography to Allow the Imaging of Noncrystalline Materials, Cells, and Single Protein Complexes

Emerging opportunities in structural biology with X-ray free-electron lasers

Three-dimensional structure determination from a single view

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