Limits...
Sub-atomic resolution X-ray crystallography and neutron crystallography: promise, challenges and potential.

Blakeley MP, Hasnain SS, Antonyuk SV - IUCrJ (2015)

Bottom Line: Although the development of neutron macromolecular crystallography over the years has been far less pronounced, and its application much less widespread, the availability of new and improved instrumentation, combined with dedicated deuteration facilities, are beginning to transform the field.Here a review of the current status of sub-atomic X-ray and neutron macromolecular crystallography is given and future prospects for combined approaches are outlined.New results from two metalloproteins, copper nitrite reductase and cytochrome c', are also included, which illustrate the type of information that can be obtained from sub-atomic-resolution (∼0.8 Å) X-ray structures, while also highlighting the need for complementary neutron studies that can provide details of H atoms not provided by X-ray crystallography.

View Article: PubMed Central - HTML - PubMed

Affiliation: Large-Scale Structures Group, Institut Laue-Langevin , 71 Avenue des Martyrs, Grenoble 38000, France.

ABSTRACT
The International Year of Crystallography saw the number of macromolecular structures deposited in the Protein Data Bank cross the 100000 mark, with more than 90000 of these provided by X-ray crystallography. The number of X-ray structures determined to sub-atomic resolution (i.e. ≤1 Å) has passed 600 and this is likely to continue to grow rapidly with diffraction-limited synchrotron radiation sources such as MAX-IV (Sweden) and Sirius (Brazil) under construction. A dozen X-ray structures have been deposited to ultra-high resolution (i.e. ≤0.7 Å), for which precise electron density can be exploited to obtain charge density and provide information on the bonding character of catalytic or electron transfer sites. Although the development of neutron macromolecular crystallography over the years has been far less pronounced, and its application much less widespread, the availability of new and improved instrumentation, combined with dedicated deuteration facilities, are beginning to transform the field. Of the 83 macromolecular structures deposited with neutron diffraction data, more than half (49/83, 59%) were released since 2010. Sub-mm(3) crystals are now regularly being used for data collection, structures have been determined to atomic resolution for a few small proteins, and much larger unit-cell systems (cell edges >100 Å) are being successfully studied. While some details relating to H-atom positions are tractable with X-ray crystallography at sub-atomic resolution, the mobility of certain H atoms precludes them from being located. In addition, highly polarized H atoms and protons (H(+)) remain invisible with X-rays. Moreover, the majority of X-ray structures are determined from cryo-cooled crystals at 100 K, and, although radiation damage can be strongly controlled, especially since the advent of shutterless fast detectors, and by using limited doses and crystal translation at micro-focus beams, radiation damage can still take place. Neutron crystallography therefore remains the only approach where diffraction data can be collected at room temperature without radiation damage issues and the only approach to locate mobile or highly polarized H atoms and protons. Here a review of the current status of sub-atomic X-ray and neutron macromolecular crystallography is given and future prospects for combined approaches are outlined. New results from two metalloproteins, copper nitrite reductase and cytochrome c', are also included, which illustrate the type of information that can be obtained from sub-atomic-resolution (∼0.8 Å) X-ray structures, while also highlighting the need for complementary neutron studies that can provide details of H atoms not provided by X-ray crystallography.

No MeSH data available.


Related in: MedlinePlus

Large crystals of perdeuterated AcNiR have been recently grown and one of the largest (∼1 mm3) is shown here.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4491318&req=5

fig6: Large crystals of perdeuterated AcNiR have been recently grown and one of the largest (∼1 mm3) is shown here.

Mentions: The largest crystal available of AcNiR with volume ∼0.3 mm3 (0.8 × 0.7 × 0.6 mm) was soaked in D2O buffers one month prior to neutron data collection, in order to exchange labile H atoms for D atoms. Using exposures from 12 to 24 h, diffraction data at RT were collected from the D-exchanged crystal to 2.3 Å resolution (Fig. 5 ▸) over a period of 15 days using LADI-III. Data were indexed and integrated using LAUEGEN (Campbell et al., 1998 ▸), wavelength-normalized using LSCALE (Arzt et al., 1999 ▸) and scaled and merged using the CCP4 program SCALA (Winn et al., 2011 ▸). Data-collection and processing statistics for the neutron data are given in Table 4 ▸. Structural refinement using the neutron data is currently in progress and will be reported elsewhere. In addition, perdeuterated AcNiR has since been produced in the Deuteration Laboratory at the ILL, and larger crystals of ∼1 mm3 have been grown (Fig. 6 ▸). In summer 2015, we hope to collect a complete data set using LADI-III on these larger perdeuterated AcNiR crystals, with the aim to extend the resolution of the diffraction data such that the visibility of all H atoms (as D atoms) in the proton pathways will be enhanced.


Sub-atomic resolution X-ray crystallography and neutron crystallography: promise, challenges and potential.

Blakeley MP, Hasnain SS, Antonyuk SV - IUCrJ (2015)

Large crystals of perdeuterated AcNiR have been recently grown and one of the largest (∼1 mm3) is shown here.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4491318&req=5

fig6: Large crystals of perdeuterated AcNiR have been recently grown and one of the largest (∼1 mm3) is shown here.
Mentions: The largest crystal available of AcNiR with volume ∼0.3 mm3 (0.8 × 0.7 × 0.6 mm) was soaked in D2O buffers one month prior to neutron data collection, in order to exchange labile H atoms for D atoms. Using exposures from 12 to 24 h, diffraction data at RT were collected from the D-exchanged crystal to 2.3 Å resolution (Fig. 5 ▸) over a period of 15 days using LADI-III. Data were indexed and integrated using LAUEGEN (Campbell et al., 1998 ▸), wavelength-normalized using LSCALE (Arzt et al., 1999 ▸) and scaled and merged using the CCP4 program SCALA (Winn et al., 2011 ▸). Data-collection and processing statistics for the neutron data are given in Table 4 ▸. Structural refinement using the neutron data is currently in progress and will be reported elsewhere. In addition, perdeuterated AcNiR has since been produced in the Deuteration Laboratory at the ILL, and larger crystals of ∼1 mm3 have been grown (Fig. 6 ▸). In summer 2015, we hope to collect a complete data set using LADI-III on these larger perdeuterated AcNiR crystals, with the aim to extend the resolution of the diffraction data such that the visibility of all H atoms (as D atoms) in the proton pathways will be enhanced.

Bottom Line: Although the development of neutron macromolecular crystallography over the years has been far less pronounced, and its application much less widespread, the availability of new and improved instrumentation, combined with dedicated deuteration facilities, are beginning to transform the field.Here a review of the current status of sub-atomic X-ray and neutron macromolecular crystallography is given and future prospects for combined approaches are outlined.New results from two metalloproteins, copper nitrite reductase and cytochrome c', are also included, which illustrate the type of information that can be obtained from sub-atomic-resolution (∼0.8 Å) X-ray structures, while also highlighting the need for complementary neutron studies that can provide details of H atoms not provided by X-ray crystallography.

View Article: PubMed Central - HTML - PubMed

Affiliation: Large-Scale Structures Group, Institut Laue-Langevin , 71 Avenue des Martyrs, Grenoble 38000, France.

ABSTRACT
The International Year of Crystallography saw the number of macromolecular structures deposited in the Protein Data Bank cross the 100000 mark, with more than 90000 of these provided by X-ray crystallography. The number of X-ray structures determined to sub-atomic resolution (i.e. ≤1 Å) has passed 600 and this is likely to continue to grow rapidly with diffraction-limited synchrotron radiation sources such as MAX-IV (Sweden) and Sirius (Brazil) under construction. A dozen X-ray structures have been deposited to ultra-high resolution (i.e. ≤0.7 Å), for which precise electron density can be exploited to obtain charge density and provide information on the bonding character of catalytic or electron transfer sites. Although the development of neutron macromolecular crystallography over the years has been far less pronounced, and its application much less widespread, the availability of new and improved instrumentation, combined with dedicated deuteration facilities, are beginning to transform the field. Of the 83 macromolecular structures deposited with neutron diffraction data, more than half (49/83, 59%) were released since 2010. Sub-mm(3) crystals are now regularly being used for data collection, structures have been determined to atomic resolution for a few small proteins, and much larger unit-cell systems (cell edges >100 Å) are being successfully studied. While some details relating to H-atom positions are tractable with X-ray crystallography at sub-atomic resolution, the mobility of certain H atoms precludes them from being located. In addition, highly polarized H atoms and protons (H(+)) remain invisible with X-rays. Moreover, the majority of X-ray structures are determined from cryo-cooled crystals at 100 K, and, although radiation damage can be strongly controlled, especially since the advent of shutterless fast detectors, and by using limited doses and crystal translation at micro-focus beams, radiation damage can still take place. Neutron crystallography therefore remains the only approach where diffraction data can be collected at room temperature without radiation damage issues and the only approach to locate mobile or highly polarized H atoms and protons. Here a review of the current status of sub-atomic X-ray and neutron macromolecular crystallography is given and future prospects for combined approaches are outlined. New results from two metalloproteins, copper nitrite reductase and cytochrome c', are also included, which illustrate the type of information that can be obtained from sub-atomic-resolution (∼0.8 Å) X-ray structures, while also highlighting the need for complementary neutron studies that can provide details of H atoms not provided by X-ray crystallography.

No MeSH data available.


Related in: MedlinePlus