Unambiguous determination of H-atom positions: comparing results from neutron and high-resolution X-ray crystallography

doi:https://doi.org/10.1107/S0907444910005494

Title: Unambiguous determination of H-atom positions: comparing results from neutron and high-resolution X-ray crystallography

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Abstract

The locations of H atoms in biological structures can be difficult to determine using X-ray diffraction methods. Neutron diffraction offers a relatively greater scattering magnitude from H and D atoms. Here, 1.65 {angstrom} resolution neutron diffraction studies of fully perdeuterated and selectively CH{sub 3}-protonated perdeuterated crystals of Pyrococcus furiosus rubredoxin (D-rubredoxin and HD-rubredoxin, respectively) at room temperature (RT) are described, as well as 1.1 {angstrom} resolution X-ray diffraction studies of the same protein at both RT and 100 K. The two techniques are quantitatively compared in terms of their power to directly provide atomic positions for D atoms and analyze the role played by atomic thermal motion by computing the {sigma} level at the D-atom coordinate in simulated-annealing composite D-OMIT maps. It is shown that 1.65 {angstrom} resolution RT neutron data for perdeuterated rubredoxin are {approx}8 times more likely overall to provide high-confidence positions for D atoms than 1.1 {angstrom} resolution X-ray data at 100 K or RT. At or above the 1.0{sigma} level, the joint X-ray/neutron (XN) structures define 342/378 (90%) and 291/365 (80%) of the D-atom positions for D-rubredoxin and HD-rubredoxin, respectively. The X-ray-only 1.1 {angstrom} resolution 100 K structures determine only 19/388 (5%) and 8/388 (2%) ofmore »« less

Authors:

Gardberg, Anna S; Del Castillo, Alexis R; Weiss, Kevin L; Meilleur, Flora; Blakeley, Matthew P; Myles, Dean A.A. ^[1]

ORNL

Publication Date:: 2010-11-19

Research Org.:: Argonne National Lab. (ANL), Argonne, IL (United States). Advanced Photon Source (APS)

Sponsoring Org.:: USDOE

OSTI Identifier:: 1002765

Resource Type:: Journal Article

Journal Name:: Acta Crystallogr. D

Additional Journal Information:: Journal Volume: 66; Journal Issue: (5) ; 05, 2010

Country of Publication:: United States

Language:: ENGLISH

Subject:: 59 BASIC BIOLOGICAL SCIENCES; 72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS; ATOMS; CRYSTALLOGRAPHY; ELECTRON DENSITY; NEUTRON DIFFRACTION; NEUTRONS; PROTEINS; RESOLUTION; RUBREDOXIN; SCATTERING; X-RAY DIFFRACTION

Citation Formats


                    Gardberg, Anna S, Del Castillo, Alexis R, Weiss, Kevin L, Meilleur, Flora, Blakeley, Matthew P, Myles, Dean A.A., and ILL). Unambiguous determination of H-atom positions: comparing results from neutron and high-resolution X-ray crystallography.  United States: N. p., 2010. 
        Web.  doi:10.1107/S0907444910005494.

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                    Gardberg, Anna S, Del Castillo, Alexis R, Weiss, Kevin L, Meilleur, Flora, Blakeley, Matthew P, Myles, Dean A.A., & ILL). Unambiguous determination of H-atom positions: comparing results from neutron and high-resolution X-ray crystallography.  United States.  https://doi.org/10.1107/S0907444910005494

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                    Gardberg, Anna S, Del Castillo, Alexis R, Weiss, Kevin L, Meilleur, Flora, Blakeley, Matthew P, Myles, Dean A.A., and ILL). Fri .  
        "Unambiguous determination of H-atom positions: comparing results from neutron and high-resolution X-ray crystallography".  United States.  https://doi.org/10.1107/S0907444910005494.

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@article{osti_1002765,

  title        = {Unambiguous determination of H-atom positions: comparing results from neutron and high-resolution X-ray crystallography},

  author       = {Gardberg, Anna S and Del Castillo, Alexis R and Weiss, Kevin L and Meilleur, Flora and Blakeley, Matthew P and Myles, Dean A.A. and ILL)},

  abstractNote = {The locations of H atoms in biological structures can be difficult to determine using X-ray diffraction methods. Neutron diffraction offers a relatively greater scattering magnitude from H and D atoms. Here, 1.65 {angstrom} resolution neutron diffraction studies of fully perdeuterated and selectively CH{sub 3}-protonated perdeuterated crystals of Pyrococcus furiosus rubredoxin (D-rubredoxin and HD-rubredoxin, respectively) at room temperature (RT) are described, as well as 1.1 {angstrom} resolution X-ray diffraction studies of the same protein at both RT and 100 K. The two techniques are quantitatively compared in terms of their power to directly provide atomic positions for D atoms and analyze the role played by atomic thermal motion by computing the {sigma} level at the D-atom coordinate in simulated-annealing composite D-OMIT maps. It is shown that 1.65 {angstrom} resolution RT neutron data for perdeuterated rubredoxin are {approx}8 times more likely overall to provide high-confidence positions for D atoms than 1.1 {angstrom} resolution X-ray data at 100 K or RT. At or above the 1.0{sigma} level, the joint X-ray/neutron (XN) structures define 342/378 (90%) and 291/365 (80%) of the D-atom positions for D-rubredoxin and HD-rubredoxin, respectively. The X-ray-only 1.1 {angstrom} resolution 100 K structures determine only 19/388 (5%) and 8/388 (2%) of the D-atom positions above the 1.0{sigma} level for D-rubredoxin and HD-rubredoxin, respectively. Furthermore, the improved model obtained from joint XN refinement yielded improved electron-density maps, permitting the location of more D atoms than electron-density maps from models refined against X-ray data only.},

  doi          = {10.1107/S0907444910005494},

  url          = {https://www.osti.gov/biblio/1002765},
  journal      = {Acta Crystallogr. D},
number       = (5) ; 05, 2010,

  volume       = 66,

  place        = {United States},

  year         = {2010},

  month        = {11}

}

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