Improving the accuracy and resolution of neutron crystallographic data by three-dimensional profile fitting of Bragg peaks in reciprocal space

It is demonstrated that using three-dimensional profile fitting of Bragg peaks increases the accuracy and resolution of neutron crystallographic data collected from proteins and reveals new features in nuclear density maps calculated from these data.

[1]  Sarah J. Cooper,et al.  Substrate Binding Induces Conformational Changes in a Class A β-lactamase That Prime It for Catalysis , 2018 .

[2]  Gwyndaf Evans,et al.  DIALS: implementation and evaluation of a new integration package , 2018, Acta crystallographica. Section D, Structural biology.

[3]  S. Hofbauer,et al.  Molecular Mechanism of Enzymatic Chlorite Detoxification: Insights from Structural and Kinetic Studies , 2017, ACS catalysis.

[4]  L. Coates,et al.  Protein crystallization and initial neutron diffraction studies of the photosystem II subunit PsbO. , 2017, Acta crystallographica. Section F, Structural biology communications.

[5]  C. Unkefer,et al.  Neutron and Atomic Resolution X-ray Structures of a Lytic Polysaccharide Monooxygenase Reveal Copper-Mediated Dioxygen Binding and Evidence for N-Terminal Deprotonation. , 2017, Biochemistry.

[6]  G. Borgstahl,et al.  Preliminary neutron diffraction analysis of challenging human manganese superoxide dismutase crystals , 2017, Acta crystallographica. Section F, Structural biology communications.

[7]  M. Gutmann A 3D profile function suitable for integration of neutron time-of-flight single crystal diffraction peaks , 2017 .

[8]  C. Unkefer,et al.  Fifteen years of the Protein Crystallography Station: the coming of age of macromolecular neutron crystallography , 2017, IUCrJ.

[9]  T. Ohhara,et al.  Application of profile fitting method to neutron time-of-flight protein single crystal diffraction data collected at the iBIX , 2016, Scientific Reports.

[10]  P. Moody,et al.  Direct visualization of a Fe(IV)–OH intermediate in a heme enzyme , 2016, Nature Communications.

[11]  K. Tomoyori,et al.  New data reduction protocol for Bragg reflections observed by TOF single-crystal neutron diffractometry for protein crystals with large unit cells , 2016 .

[12]  W. B. O’Dell,et al.  Neutron protein crystallography: A complementary tool for locating hydrogens in proteins. , 2016, Archives of biochemistry and biophysics.

[13]  K. Weiss,et al.  Neutron diffraction analysis of Pseudomonas aeruginosa peptidyl-tRNA hydrolase 1. , 2016, Acta crystallographica. Section F, Structural biology communications.

[14]  D. Graham,et al.  Direct determination of protonation states and visualization of hydrogen bonding in a glycoside hydrolase with neutron crystallography , 2015, Proceedings of the National Academy of Sciences.

[15]  R. Riedel,et al.  Design and performance of a large area neutron sensitive anger camera , 2015 .

[16]  E. Iverson,et al.  The Macromolecular Neutron Diffractometer MaNDi at the Spallation Neutron Source , 2015 .

[17]  P. F. Peterson,et al.  Mantid - Data Analysis and Visualization Package for Neutron Scattering and $μ SR$ Experiments , 2014, 1407.5860.

[18]  P. Moody,et al.  Neutron cryo-crystallography captures the protonation state of ferryl heme in a peroxidase , 2014, Science.

[19]  P. F. Peterson,et al.  Integration of neutron time-of-flight single-crystal Bragg peaks in reciprocal space , 2014 .

[20]  K. Diederichs,et al.  Better models by discarding data? , 2013, Acta crystallographica. Section D, Biological crystallography.

[21]  P. Andrew Karplus,et al.  Linking Crystallographic Model and Data Quality , 2012, Science.

[22]  P. Zwart,et al.  Towards automated crystallographic structure refinement with phenix.refine , 2012, Acta crystallographica. Section D, Biological crystallography.

[23]  M. Mustyakimov,et al.  High-resolution neutron crystallographic studies of the hydration of the coenzyme cob(II)alamin. , 2011, Acta crystallographica. Section D, Biological crystallography.

[24]  Matthew J. Frost,et al.  CrystalPlan: an experiment-planning tool for crystallography , 2011 .

[25]  Philip R. Evans,et al.  An introduction to data reduction: space-group determination, scaling and intensity statistics , 2011, Acta crystallographica. Section D, Biological crystallography.

[26]  Paul D Adams,et al.  Joint X-ray and neutron refinement with phenix.refine. , 2010, Acta crystallographica. Section D, Biological crystallography.

[27]  Jonathan A. Cooper,et al.  Neutron diffraction studies of a class A beta-lactamase Toho-1 E166A/R274N/R276N triple mutant. , 2010, Journal of molecular biology.

[28]  Randy J. Read,et al.  Acta Crystallographica Section D Biological , 2003 .

[29]  W. Kabsch XDS , 2010, Acta crystallographica. Section D, Biological crystallography.

[30]  Jon Cooper,et al.  The catalytic mechanism of an aspartic proteinase explored with neutron and X-ray diffraction. , 2008, Journal of the American Chemical Society.

[31]  Raul Cachau,et al.  Quantum model of catalysis based on a mobile proton revealed by subatomic x-ray and neutron diffraction studies of h-aldose reductase , 2008, Proceedings of the National Academy of Sciences.

[32]  K. Lefmann,et al.  Monte Carlo simulations of neutron-scattering instruments using McStas , 2000 .

[33]  A G Leslie,et al.  Biological Crystallography Integration of Macromolecular Diffraction Data , 2022 .

[34]  J. Pflugrath,et al.  The finer things in X-ray diffraction data collection. , 1999, Acta crystallographica. Section D, Biological crystallography.

[35]  G. Artioli,et al.  Profile‐Fitting Treatment of Single‐Crystal Diffraction Data , 1996 .

[36]  J. W. Campbell LAUEGEN, an X-windows-based program for the processing of Laue diffraction data , 1995 .

[37]  G. McIntyre,et al.  Integration of single‐crystal reflections using area multidetectors , 1988 .

[38]  S. Ikeda,et al.  Wide-energy-range, high-resolution measurements of neutron pulse shapes of polyethylene moderators , 1985 .

[39]  A. Wlodawer,et al.  Improved technique for peak integration for crystallographic data collected with position‐sensitive detectors: a dynamic mask procedure , 1981 .

[40]  G. S. Smith,et al.  Single‐crystal intensity measurements with the three‐circle counter diffractometer , 1962 .

[41]  Wolfgang Kabsch,et al.  Integration, scaling, space‐group assignment and post refinement , 2006 .

[42]  Z. Otwinowski,et al.  [20] Processing of X-ray diffraction data collected in oscillation mode. , 1997, Methods in enzymology.

[43]  S. Harrison,et al.  [19] Oscillation method with large unit cells , 1985 .

[44]  M. Rossmann Determining the intensity of Bragg reflections from oscillation photographs. , 1985, Methods in enzymology.

[45]  R Diamond,et al.  Profile analysis in single crystal diffractometry. , 1969, Acta crystallographica. Section A, Crystal physics, diffraction, theoretical and general crystallography.