Acta Crystallographica Section D

Biological Crystallography

Volume 66, Part 4 (April 2010)


Experimental phasing and radiation damage

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: Speakers at the CCP4 Study Weekend 2009. Front row, left to right: James Holton, Arwen Pearson, Zbigniew Dauter, Elspeth Garman, Tobias Beck, Zbyszek Otwinowski. Middle row, left to right: Alexander Popov, Sean McSweeney, Garry Taylor, Helen Walden, Karthik Paithankar, Marc Schiltz, Gerard Bricogne. Back row, left to right: Kevin Cowtan, Martin Weik, Clemens Vonrhein, Peter Sun, Douglas Juers, George Sheldrick, Susan Lea, Airlie McCoy.

research papers


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Acta Cryst. (2010). D66, 325-338  [ doi:10.1107/S0907444910006694 ]

Introduction to phasing

G. L. Taylor

Synopsis: This introductory paper to the CCP4 weekend on experimental phasing introduces the concept of the `phase problem' for non-experts. Modern methods of phasing are explored, including some recent examples that can be downloaded as tutorials.

Online 24 March 2010


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Acta Cryst. (2010). D66, 339-351  [ doi:10.1107/S0907444910008656 ]

Radiation damage in macromolecular crystallography: what is it and why should we care?

E. F. Garman

Synopsis: The basic causes of the radiation damage inflicted on macromolecular crystals during diffraction experiments are summarized, as well as the current state of research which attempts to understand and to mitigate it.

Online 24 March 2010


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Acta Cryst. (2010). D66, 352-357  [ doi:10.1107/S0907444909038207 ]

Selenium incorporation using recombinant techniques

H. Walden

Synopsis: An overview of techniques for recombinant incorporation of selenium and subsequent purification and crystallization of the resulting labelled protein.

Online 24 March 2010


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Acta Cryst. (2010). D66, 358-365  [ doi:10.1107/S0907444909053074 ]

A rational approach to heavy-atom derivative screening

M. G. Joyce, S. Radaev and P. D. Sun

Synopsis: In order to overcome the difficulties associated with the `classical' heavy-atom derivatization procedure, an attempt has been made to develop a rational crystal-free heavy-atom-derivative screening method and a quick-soak derivatization procedure which allows heavy-atom compound identification.

Online 24 March 2010


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Acta Cryst. (2010). D66, 366-373  [ doi:10.1107/S090744490903995X ]

Progress in rational methods of cryoprotection in macromolecular crystallography

T. Alcorn and D. H. Juers

Synopsis: Measurements of the average thermal contractions (294[rightwards arrow]72 K) of 26 different cryosolutions are presented and discussed in conjunction with other recent advances in the rational design of protocols for cryogenic cooling in macromolecular crystallography.

Online 24 March 2010


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Acta Cryst. (2010). D66, 374-380  [ doi:10.1107/S0907444909051609 ]

The magic triangle goes MAD: experimental phasing with a bromine derivative

T. Beck, T. Gruene and G. M. Sheldrick

Synopsis: 5-Amino-2,4,6-tribromoisophthalic acid is used as a phasing tool for protein structure determination by MAD phasing. It is the second representative of a novel class of compounds for heavy-atom derivatization that combine heavy atoms with amino and carboxyl groups for binding to proteins.

PDB references: 3gt3 and 3gt4

Online 24 March 2010


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Acta Cryst. (2010). D66, 381-388  [ doi:10.1107/S0907444910006724 ]

Know your dose: RADDOSE

K. S. Paithankar and E. F. Garman

Synopsis: The program RADDOSE computes the dose absorbed by a macromolecular crystal and here a guide is provided to help to ensure the proper use of the program. In the new version (v.3) described here, modifications to include the energy deposited owing to Compton scattering have been made.

Online 24 March 2010


 

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Acta Cryst. (2010). D66, 389-392  [ doi:10.1107/S0907444909038578 ]

Carrying out an optimal experiment

Z. Dauter

Synopsis: Diffraction data collection parameters leading to optimal data quality are discussed in the context of different applications of these data.

Online 24 March 2010


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[HTML version][PDF version][Supplementary Material]  [Open access]

Acta Cryst. (2010). D66, 393-408  [ doi:10.1107/S0907444910007262 ]

The minimum crystal size needed for a complete diffraction data set

J. M. Holton and K. A. Frankel

Synopsis: A formula for absolute scattering power is derived to include spot fading arising from radiation damage and the crystal volume needed to collect diffraction data to a given resolution is calculated.

Online 24 March 2010


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Acta Cryst. (2010). D66, 409-419  [ doi:10.1107/S0907444909054961 ]

Optimization of data collection taking radiation damage into account

G. P. Bourenkov and A. N. Popov

Synopsis: Software implementing a new method for the optimal choice of data-collection parameters, accounting for the effects of radiation damage, is presented.

Online 24 March 2010


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Acta Cryst. (2010). D66, 420-425  [ doi:10.1107/S0907444909048112 ]

With phases: how two wrongs can sometimes make a right

P. Roversi, S. Johnson and S. M. Lea

Synopsis: Combining experimental phases and those from refinement of very incomplete models significantly improves electron-density maps.

Online 24 March 2010


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Acta Cryst. (2010). D66, 426-436  [ doi:10.1107/S0907444909040177 ]

Diffraction data analysis in the presence of radiation damage

D. Borek, M. Cymborowski, M. Machius, W. Minor and Z. Otwinowski

Synopsis: Radiation-induced decay of crystal diffraction and additional specific chemical changes of macromolecules forming the crystal lattice are currently two of the main limiting factors in the acquisition of macromolecular diffraction data and macromolecular structure determination. Data-processing and phasing protocols are discussed in the context of radiation-induced changes.

Online 24 March 2010


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Acta Cryst. (2010). D66, 437-446  [ doi:10.1107/S0907444910002702 ]

Temperature-dependent macromolecular X-ray crystallography

M. Weik and J.-P. Colletier

Synopsis: The dynamical behaviour of crystalline macromolecules and their surrounding solvent as a function of cryo-temperature is reviewed.

Online 24 March 2010


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Acta Cryst. (2010). D66, 447-457  [ doi:10.1107/S0907444909053578 ]

`Broken symmetries' in macromolecular crystallography: phasing from unmerged data

M. Schiltz and G. Bricogne

Synopsis: Site-specific radiation damage and anisotropy of anomalous scattering can induce intensity differences in symmetry-related reflections. If the data are kept unmerged, these symmetry-breaking effects can become a source of phase information.

Online 24 March 2010


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[HTML version][PDF version][Supplementary Material]  [Open access]

Acta Cryst. (2010). D66, 458-469  [ doi:10.1107/S0907444910006335 ]

Experimental phasing: best practice and pitfalls

A. J. McCoy and R. J. Read

Synopsis: The pitfalls of experimental phasing are described.

Online 24 March 2010


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[HTML version][PDF version][Supplementary Material]  [Open access]

Acta Cryst. (2010). D66, 470-478  [ doi:10.1107/S090744490903947X ]

Recent developments in classical density modification

K. Cowtan

Synopsis: Several new methods are evaluated for use in the improvement of experimental phases in the framework of a classical density-modification calculation. These methods have been implemented in a new computer program, Parrot.

Online 24 March 2010


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Acta Cryst. (2010). D66, 479-485  [ doi:10.1107/S0907444909038360 ]

Experimental phasing with SHELXC/D/E: combining chain tracing with density modification

G. M. Sheldrick

Synopsis: Experimental phasing with SHELXC/D/E has been enhanced by the incorporation of main-chain tracing into the iterative density modification; this also provides a simple and effective way of exploiting noncrystallographic symmetry.

Online 24 March 2010


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Acta Cryst. (2010). D66, 486-501  [ doi:10.1107/S0907444910007493 ]

Features and development of Coot

P. Emsley, B. Lohkamp, W. G. Scott and K. Cowtan

Synopsis: Coot is a molecular-graphics program designed to assist in the building of protein and other macromolecular models. The current state of development and available features are presented.

Online 24 March 2010


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