Macromolecular crystal twinning, lattice disorders and multiple crystals1

Helliwell, John R.

doi:10.1080/08893110802360925

Cited by 29 publications

(19 citation statements)

References 110 publications

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“…A preliminary crystallographic data analysis is performed in order to detect and ignore potential reflection outliers (Read, 1999). If twinning (for a review, see Parsons, 2003;Helliwell, 2008) is suspected, a user can run phenix.…”

Section: Initial Step Of Refinement: Processing Of Inputsmentioning

confidence: 99%

Towards automated crystallographic structure refinement with phenix.refine

Afonine

Grosse‐Kunstleve

Echols

et al. 2012

Acta Crystallogr D Biol Crystallogr

4,965

4,406

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phenix.refine is a program within the PHENIX package that supports crystallographic structure refinement against experimental data with a wide range of upper resolution limits using a large repertoire of model parameterizations. It has several automation features and is also highly flexible. Several hundred parameters enable extensive customizations for complex use cases. Multiple user-defined refinement strategies can be applied to specific parts of the model in a single refinement run. An intuitive graphical user interface is available to guide novice users and to assist advanced users in managing refinement projects. X-ray or neutron diffraction data can be used separately or jointly in refinement. phenix.refine is tightly integrated into the PHENIX suite, where it serves as a critical component in automated model building, final structure refinement, structure validation and deposition to the wwPDB. This paper presents an overview of the major phenix.refine features, with extensive literature references for readers interested in more detailed discussions of the methods.

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Section: Initial Step Of Refinement: Processing Of Inputsmentioning

confidence: 99%

Towards automated crystallographic structure refinement with phenix.refine

Afonine

Grosse‐Kunstleve

Echols

et al. 2012

Acta Crystallogr D Biol Crystallogr

4,965

4,406

View full text Add to dashboard Cite

show abstract

“…Crystal-growth disorders can lead to various problems in the analysis of diffraction data. Types that have been studied in macromolecular crystals include twinning (Yeates, 1997;Parsons, 2003;Helliwell, 2008), in which distinct threedimensional domains of a crystal are oriented differently but are otherwise well ordered individually, and various types of disorder that occur over shorter length scales in a crystal (e.g. from unit cell to unit cell).…”

Section: Introductionmentioning

confidence: 99%

Analysis of lattice-translocation disorder in the layered hexagonal structure of carboxysome shell protein CsoS1C

Tsai

Sawaya²,

Yeates³

2009

Acta Crystallogr D Biol Cryst

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Lattice-translocation or crystal order-disorder phenomena occur when some layers or groups of molecules in a crystal are randomly displaced relative to other groups of molecules by a discrete set of vectors. In previous work, the effects of lattice translocation on diffraction intensities have been corrected by considering that the observed intensities are the product of the intensities from an ideal crystal (lacking disorder) multiplied by the squared magnitude of the Fourier transform of the set of translocation vectors. Here, the structure determination is presented of carboxysome protein CsoS1C from Halothiobacillius neapolitanus in a crystal exhibiting a lattice translocation with unique features. The diffraction data are fully accounted for by a crystal unit cell composed of two layers of cyclic protein hexamers. The first layer is fully ordered (i.e. has one fixed position), while the second layer randomly takes one of three alternative positions whose displacements are related to each other by threefold symmetry. Remarkably, the highest symmetry present in the crystal is P3, yet the intensity data (and the Patterson map) obey 6/m instead of \overline 3 symmetry; the intensities exceed the symmetry expected from combining the crystal space group with an inversion center. The origin of this rare phenomenon, known as symmetry enhancement, is discussed and shown to be possible even for a perfectly ordered crystal. The lattice-translocation treatment described here may be useful in analyzing other cases of disorder in which layers or groups of molecules are shifted in multiple symmetry-related directions.

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“…It is well known that the twinning activity increases as the additive amounts decrease [30]. Because the twinning activity in hcp metals plays a significant role in the deformation behavior such as the stress-strain curve and evolution of the Lankford value, as reported in previous studies on Mg alloys [20,[31][32], the deformation behavior in Grade 1 sheets should differ greatly from that of Grade 2 sheets.…”

Section: Introductionmentioning

confidence: 92%

Anisotropic deformation behavior under various strain paths in commercially pure titanium Grade 1 and Grade 2 sheets

Hama

Kobuki

et al. 2016

Materials Science and Engineering: A

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In this study, the anisotropic deformation behavior in commercially pure titanium Grade 1 and Grade 2 sheets under various strain paths was examined. A small but sharp stress peak arose during tension following compression in the Grade 1 sheet when loaded in the rolling direction, and the occurrence of a stress peak was retarded when the sheet was subjected to cyclic loading; however, such behavior did not occur in the Grade 2 sheet. Similarly, the work-hardening rate was different between the initial and latter stages of compression following tension. These behaviors did not arise when the sheets were loaded in other directions. The type of active twin mode was different depending on the loading path. When loaded in the rolling direction in both Grade 1 and Grade 2 sheets, <101 � 2> twinning and detwinning were active, respectively, during compression and tension following compression, whereas <112 � 2> twinning and detwinning were active during tension and compression following tension. The twinning activity was much more pronounced in the Grade 1 sheet than in the Grade 2 sheet. The abovementioned stress-strain responses were presumed to result from twinning and detwinning activities as for magnesium alloy sheets.However, we concluded that the effect of twinning activity on the stress-strain curves was much smaller in the titanium sheet than in magnesium alloy sheets.

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Macromolecular crystal twinning, lattice disorders and multiple crystals1

Cited by 29 publications

References 110 publications

Towards automated crystallographic structure refinement with phenix.refine

Towards automated crystallographic structure refinement with phenix.refine

Analysis of lattice-translocation disorder in the layered hexagonal structure of carboxysome shell protein CsoS1C

Anisotropic deformation behavior under various strain paths in commercially pure titanium Grade 1 and Grade 2 sheets

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