Impact of synchrotron radiation on macromolecular crystallography: a personal view

Dauter, Zbigniew; Jaskólski, Mariusz; Wlodawer, Alexander

doi:10.1107/s0909049510011611

Cited by 38 publications

(106 citation statements)

References 73 publications

(86 reference statements)

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“…The current and developing state of the art of X-ray diffraction promises more high-resolution, high-quality data of proteins in the future (Duke & Johnson, 2010;Dauter et al, 2010;Mueller et al, 2012;Garman & Weik, 2013). One factor limiting the number of very high-resolution data sets in the Protein Data Bank (PDB; Berman et al, 2000) is the geometry of many diffractometers for protein diffraction.…”

Section: Introductionmentioning

confidence: 99%

The active site of hen egg-white lysozyme: flexibility and chemical bonding

Held¹,

Smaalen²

2014

Acta Crystallogr D Biol Crystallogr

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Chemical bonding at the active site of hen egg-white lysozyme (HEWL) is analyzed on the basis of Bader's quantum theory of atoms in molecules [QTAIM;Bader (1994), Atoms in Molecules: A Quantum Theory. Oxford University Press] applied to electron-density maps derived from a multipole model. The observation is made that the atomic displacement parameters (ADPs) of HEWL at a temperature of 100 K are larger than ADPs in crystals of small biological molecules at 298 K. This feature shows that the ADPs in the cold crystals of HEWL reflect frozen-in disorder rather than thermal vibrations of the atoms. Directly generalizing the results of multipole studies on small-molecule crystals, the important consequence for electron-density analysis of protein crystals is that multipole parameters cannot be independently varied in a meaningful way in structure refinements. Instead, a multipole model for HEWL has been developed by refinement of atomic coordinates and ADPs against the X-ray diffraction data of Wang and coworkers [Wang et al. (2007), Acta Cryst. D63, 1254-1268], while multipole parameters were fixed to the values for transferable multipole parameters from the ELMAM2 database [Domagala et al. (2012), Acta Cryst. A68, 337-351] . Static and dynamic electron densities based on this multipole model are presented. Analysis of their topological properties according to the QTAIM shows that the covalent bonds possess similar properties to the covalent bonds of small molecules. Hydrogen bonds of intermediate strength are identified for the Glu35 and Asp52 residues, which are considered to be essential parts of the active site of HEWL. Furthermore, a series of weak C-HÁ Á ÁO hydrogen bonds are identified by means of the existence of bond critical points (BCPs) in the multipole electron density. It is proposed that these weak interactions might be important for defining the tertiary structure and activity of HEWL. The deprotonated state of Glu35 prevents a distinction between the Phillips and Koshland mechanisms.

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Section: Introductionmentioning

confidence: 99%

The active site of hen egg-white lysozyme: flexibility and chemical bonding

Held¹,

Smaalen²

2014

Acta Crystallogr D Biol Crystallogr

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“…Mason-Pzer Monkey Virus protease [26], [27], (5) not processed due to the license problem, (6,7) Two forms of NRAD extracted from one dataset.…”

Section: Resultsmentioning

confidence: 99%

Data Processing Programs for Analysis of Diffraction Images of Macromolecular Crystals Recorded using Synchrotron Radiation

Gilski

2012

Acta Phys. Pol. A

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Besides the crystal preparation, the rst and crucial step in the process of protein structure determination is proper processing of the collected diraction images, as they provide the experimental observations used throughout the entire process of structure solution and renement. In the last two decades several computer programs have been developed. Among the most used and popular are: HKL2000, MOSFLM, d*TREK and XDS package. To nd out the advantages and disadvantages of the data processing programs, several very dierent data sets, including diraction data from DNA/RNA and protein crystals were tested. It has been found that all the major programs for processing and analysis of diraction data give excellent and comparable results with good quality, medium resolution data sets, but their treatment of very high resolution or imperfect data diers in terms of indexing, spot integration, scaling and the treatment of errors. If the diraction data are of good quality and the problem is relatively straightforward, the automated approach to data processing may be most appropriate. On the other hand, if one is trying to squeeze out as much information from the experimental data as possible, then only expert manual processing can be successful, regardless of the data quality.

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“…Protein crystallography is now a mainstream research technique and the rate of structure deposition in the Protein Data Bank keeps increasing (AbadZapatero, 2012). Nevertheless, despite much automation, data collection remains a nontrivial experiment that requires diligent planning and careful checks, while the brightness and brilliance of third-generation synchrotrons pose a whole additional set of challenges (Chavas et al, 2012;Dauter et al, 2010;Fodje et al, 2012;Gabadinho et al, 2010;Gonzá lez et al, 2008;McCarthy et al, 2009). The availability of ever smaller and brighter beams has boosted the field on the one hand, but it has also increased the requirement of the experimenter to make the correct choices at the beamline.…”

Section: Introductionmentioning

confidence: 99%

Squeezing the most from every crystal: the fine details of data collection

Krojer¹,

Pike²,

Delft³

2013

Acta Crystallogr D Biol Cryst

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Modern synchrotron beamlines offer instrumentation of unprecedented quality, which in turn encourages increasingly marginal experiments, and for these, as much as ever, the ultimate success of data collection depends on the experience, but especially the care, of the experimenter. A representative set of difficult cases has been encountered at the Structural Genomics Consortium, a worldwide structural genomics initiative of which the Oxford site currently deposits three novel human structures per month. Achieving this target relies heavily on frequent visits to the Diamond Light Source, and the variety of crystal systems still demand customized data collection, diligent checks and careful planning of each experiment. Here, an overview is presented of the techniques and procedures that have been refined over the years and that are considered synchrotron best practice.

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Impact of synchrotron radiation on macromolecular crystallography: a personal view

Cited by 38 publications

References 73 publications

The active site of hen egg-white lysozyme: flexibility and chemical bonding

The active site of hen egg-white lysozyme: flexibility and chemical bonding

Data Processing Programs for Analysis of Diffraction Images of Macromolecular Crystals Recorded using Synchrotron Radiation

Squeezing the most from every crystal: the fine details of data collection

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