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Acta Crystallographica Section D

Biological Crystallography

Volume 65, Part 2 (February 2009)


Low-resolution structure determination and validation

Proceedings of the CCP4 study weekend

[Buy print version] A printed copy of this issue is available for purchase

[Preface]
[Issue Author Index][Volume Author Index]
[Cover illustration] Cover illustration: Crystallographic studies of the fungal fatty acid synthase (FAS) multienzyme (p. 101). Homologous structures of individual catalytic domains were initially fitted into a 5 Å resolution electron-density map. Phase extension to higher resolution allowed building and refinement of the atomic FAS structure shown in the background.

research papers


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Acta Cryst. (2009). D65, 101-111  [ doi:10.1107/S0907444909000778 ]

Imperfect pseudo-merohedral twinning in crystals of fungal fatty acid synthase

S. Jenni and N. Ban

Synopsis: A case of imperfect pseudo-merohedral twinning in monoclinic crystals of fungal fatty acid synthase is discussed. A space-group transition during crystal dehydration resulted in a Moiré pattern-like interference of the twinned diffraction patterns.

Online 20 January 2009


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Acta Cryst. (2009). D65, 112-120  [ doi:10.1107/S0907444908039875 ]

Structure-function studies of the RNA polymerase II elongation complex

F. Brueckner, K.-J. Armache, A. Cheung, G. E. Damsma, H. Kettenberger, E. Lehmann, J. Sydow and P. Cramer

Synopsis: X-ray crystallographic and complementary functional studies have contributed significantly to the current understanding of gene transcription. Here, recent structure-function studies on various aspects of the elongation phase of transcription are summarized.

Online 20 January 2009


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Acta Cryst. (2009). D65, 121-127  [ doi:10.1107/S0907444908040006 ]

Model-building strategies for low-resolution X-ray crystallographic data

A. M. Karmali, T. L. Blundell and N. Furnham

Synopsis: Interpretation of low-resolution X-ray crystallographic data can prove to be a difficult task. The challenges faced in electron-density interpretation, the strategies that have been employed to overcome them and developments to automate the process are reviewed.

Online 20 January 2009


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Acta Cryst. (2009). D65, 128-133  [ doi:10.1107/S0907444908043795 ]

X-ray structure determination at low resolution

A. T. Brunger, B. DeLaBarre, J. M. Davies and W. I. Weis

Synopsis: Refinement is meaningful even at 4 Å or lower, but with present methodologies it should start from high-resolution crystal structures whenever possible.

Online 20 January 2009


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Acta Cryst. (2009). D65, 134-139  [ doi:10.1107/S090744490900081X ]

On vital aid: the why, what and how of validation

G. J. Kleywegt

Synopsis: The need for validation of macromolecular crystal structures is discussed. A general approach to validation is presented, together with examples of its implementation in the special case of macromolecular crystallography.

Online 20 January 2009


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Acta Cryst. (2009). D65, 140-147  [ doi:10.1107/S0907444908041085 ]

Case-controlled structure validation

R. J. Read and G. J. Kleywegt

Synopsis: A case-matched control protocol provides a useful method to compare sets of macromolecular structures.

Online 20 January 2009


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Acta Cryst. (2009). D65, 148-155  [ doi:10.1107/S090744490804362X ]

Structure validation in chemical crystallography

A. L. Spek

Synopsis: This paper reports on the current status of structure validation in chemical crystallography.

Online 20 January 2009


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Acta Cryst. (2009). D65, 156-168  [ doi:10.1107/S0907444909001905 ]

Analysis and validation of carbohydrate three-dimensional structures

T. Lütteke

Synopsis: The article summarizes the information that is gained from and the errors that are found in carbohydrate structures in the Protein Data Bank. Validation tools that can locate these errors are described.

Online 20 January 2009


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Acta Cryst. (2009). D65, 169-175  [ doi:10.1107/S0907444908020039 ]

Prospects for de novo phasing with de novo protein models

R. Das and D. Baker

Synopsis: In a first systematic exploration of phasing with Rosetta de novo models, it is shown that all-atom refinement of coarse-grained models significantly improves both the model quality and performance in molecular replacement with the Phaser software.

Online 20 January 2009


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Acta Cryst. (2009). D65, 176-185  [ doi:10.1107/S0907444908037591 ]

Re-refinement from deposited X-ray data can deliver improved models for most PDB entries

R. P. Joosten, T. Womack, G. Vriend and G. Bricogne

Synopsis: An evaluation of validation and real-space intervention possibilities for improving existing automated (re-)refinement methods.

Online 20 January 2009


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Acta Cryst. (2009). D65, 186-192  [ doi:10.1107/S0907444908036640 ]

An emerging consensus for the structure of EmrE

V. M. Korkhov and C. G. Tate

Synopsis: The ongoing story of the structure of EmrE, the archetypical member of the small multidrug-resistance family, is described.

Online 20 January 2009


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Acta Cryst. (2009). D65, 193-199  [ doi:10.1107/S0907444909001292 ]

Analysis of errors in the structure determination of MsbA

P. D. Jeffrey

Synopsis: An analysis is presented of the methodological errors that led to the incorrect structure of MsbA.

Online 20 January 2009


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