skip to main content
OSTI.GOV title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: Rapid visualization of hydrogen positions in neutron protein crystallography structures

Journal Article · · Acta Crystallographica Section D: Biological Crystallography

Neutron crystallography is a powerful technique to visualize experimentally the position of light atoms, including hydrogen and its isotope deuterium. Over the last several years, structural biologists have shown an increasing interest for the technique as it uniquely complements X-ray crystallographic data by revealing the position of hydrogen/deuterium atoms in macromolecules. With this regained interest, access to macromolecule neutron crystallography beam lines is becoming a limiting step. In this report we show that rapid data collection could be a valuable alternative to long data collection time when appropriate. Comparison of perdeuterated Rubredoxin structures refined against neutron data sets collected over hours and up to five days shows that rapid neutron data collection in just 14 hours is sufficient to provide the position of 262 hydrogen positions atoms without ambiguity.

Research Organization:
Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)
Sponsoring Organization:
USDOE
DOE Contract Number:
AC05-00OR22725
OSTI ID:
1042841
Journal Information:
Acta Crystallographica Section D: Biological Crystallography, Vol. 68, Issue 1
Country of Publication:
United States
Language:
English

References (45)

A neutron crystallographic analysis of a rubredoxin mutant at 1.6 Å resolution journal July 2004
Protein crystallography with spallation neutrons: the user facility at Los Alamos Neutron Science Center journal January 2004
Carrying out an optimal experiment journal March 2010
LAUEGEN version 6.0 and INTLDM journal June 1998
Neutron Laue diffraction in macromolecular crystallography journal December 1997
Comparison of hydrogen determination with X-ray and neutron crystallography in a human aldose reductase–inhibitor complex journal April 2006
Neutron macromolecular crystallography with LADI-III journal October 2010
Rapid neutron-diffraction data collection for hydrogen-bonding studies: application of the Laue diffractometer (LADI) to the case study zinc (tris)thiourea sulfate journal June 2001
A quasi-Laue neutron crystallographic study of d-xylose isomerase journal May 2006
New sources and instrumentation for neutrons in biology journal April 2008
Overview of the CCP 4 suite and current developments journal March 2011
The recording and analysis of synchrotron X-radiation Laue diffraction photographs journal October 1989
Neutron structure analysis using the IBARAKI biological crystal diffractometer (iBIX) at J-PARC journal October 2010
Neutron structure of type-III antifreeze protein allows the reconstruction of AFP-ice interface journal April 2011
Unambiguous determination of H-atom positions: comparing results from neutron and high-resolution X-ray crystallography journal April 2010
Low-barrier hydrogen bond in photoactive yellow protein journal January 2009
A preliminary neutron diffraction study of rasburicase, a recombinant urate oxidase enzyme, complexed with 8-azaxanthin
  • Budayova-Spano, Monika; Bonneté, Françoise; Ferté, Natalie
  • Acta Crystallographica Section F Structural Biology and Crystallization Communications, Vol. 62, Issue 3 https://doi.org/10.1107/S1744309106006439
journal February 2006
Structure of HIV-1 protease in complex with potent inhibitor KNI-272 determined by high-resolution X-ray and neutron crystallography journal March 2009
Features and development of Coot journal March 2010
Metal Ion Roles and the Movement of Hydrogen during Reaction Catalyzed by D-Xylose Isomerase: A Joint X-Ray and Neutron Diffraction Study journal June 2010
Deuterium Labeling for Neutron Structure-Function-Dynamics Analysis book January 2009
Neutron Laue macromolecular crystallography journal August 2006
Quantum model of catalysis based on a mobile proton revealed by subatomic x-ray and neutron diffraction studies of h-aldose reductase journal February 2008
Crystal structure of rubredoxin from Pyrococcus furiosus at 0.95 Å resolution, and the structures of N-terminal methionine and formylmethionine variants of Pf Rd. Contributions of N-terminal interactions to thermostability journal October 1998
PHENIX : building new software for automated crystallographic structure determination journal October 2002
The macromolecular neutron diffractometer (MaNDi) at the Spallation Neutron Source, Oak Ridge: enhanced optics design, high-resolution neutron detectors and simulated diffraction journal April 2010
The 15-K neutron structure of saccharide-free concanavalin A journal November 2004
Neutron crystallography: opportunities, challenges, and limitations journal October 2008
Characterization of image plates for neutron diffraction journal August 2009
CrystalPlan : an experiment-planning tool for crystallography journal March 2011
LSCALE – the new normalization, scaling and absorption correction program in the Daresbury Laue software suite journal June 1999
Production and X-ray crystallographic analysis of fully deuterated cytochrome P450cam journal April 2005
Preliminary neutron crystallographic analysis of selectively CH 3 -protonated deuterated rubredoxin from Pyrococcus furiosus journal May 2008
The active site protonation states of perdeuterated Toho-1 β-lactamase determined by neutron diffraction support a role for Glu166 as the general base in acylation journal December 2010
Joint X-ray and neutron refinement with phenix.refine journal October 2010
Remarks about protein structure precision journal March 1999
Macromolecular neutron crystallography at the Protein Crystallography Station (PCS) journal October 2010
Neutron crystallographic study on rubredoxin from Pyrococcus furiosus by BIX-3, a single-crystal diffractometer for biomacromolecules journal July 2004
A high-performance neutron diffractometer for biological crystallography (BIX-3) journal January 2002
Neutron Structure of Human Carbonic Anhydrase II: Implications for Proton Transfer journal January 2010
Neutron protein crystallography: current status and a brighter future journal October 2006
Enhanced visibility of hydrogen atoms by neutron crystallography on fully deuterated myoglobin journal March 2000
Neutron Diffraction Studies of a Class A β-Lactamase Toho-1 E166A/R274N/R276N Triple Mutant journal March 2010
Rearrangement of Cruickshank's formulae for the diffraction-component precision index journal April 2002
Conceptual design of a macromolecular neutron diffractometer (MaNDi) for the SNS journal November 2005