Improvement of anisotropic displacement parameters from invariom-model refinements for three L-hydroxylysine structures

Abstract

Three L-hydroxylysine structures have been determined at 100 K by single-crystal X-ray diffraction. High-resolution data using either a laboratory or synchrotron source were collected and subjected to invariom- and independent atom-model (IAM) refinements. Anisotropic displacement parameters (ADPs) obtained from invariom refinement were compared (i) with results from a full multipole and (ii) with an IAM high-order refinement. Differences were visualized with the program PEANUT and were complemented by quantitative results from a Hirshfeld test. Influences of scale factor differences, and of refinement against F;2 versus F, have been investigated. Systematic errors were observed in the IAM, especially when only low-order data were available. Although these errors were reduced in high-order IAM refinements, they only disappeared in charge density--and likewise--invariom refinements.

On the temperature dependence of H-Uisoin the riding hydrogen model

“…Values for the hydrogen ADPs from multi-temperature single-crystal X-ray diffraction evaluated with the independent-atom model (IAM) cannot reach the accuracy achievable by neutron diffraction. To improve the physical significance of ADPs and their accuracy from X-ray diffraction (Jelsch et al, 1998;Dittrich et al, 2008), we therefore performed aspherical-atom refinements [either Hirshfeld-atom (Jayatilaka & Dittrich, 2008) or invariom refinement (Dittrich et al, 2004), see below]. QM/MM and MO/MO quantum mechanical cluster calculations (for details of how to run such computations see Dittrich et al, 2012) yield normal modes within the 'molecular Einstein approximation'.…”

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

“…Instead, useful information about the redistribution of electron density owing to chemical bonding can be obtained from refinements of atomic coordinates and ADPs of structure models incorporating multipole parameters fixed to values from a database of transferable multipole parameters, as is presented here for the ELMAM2 model of HEWL (Jelsch et al, 1998;Dittrich et al, 2008;Dominiak et al, 2009;Domagała et al, 2012).…”

“…This holds true for a multipole model with multipole parameters fixed to values from a database (Afonine et al, 2004;Dittrich et al, 2005Dittrich et al, , 2008 smaller than ADPs in the corresponding IAM. This feature is explained by electron density in covalent bonds being mimicked by increased values of ADPs, while it is explicitly present in the aspherical scattering factors of the multipole model.…”

“…Instead, the refinement of multipole models is only meaningful with the multipole parameters fixed to values from a database (Jelsch et al, 1998;Dittrich et al, 2008;Dominiak et al, 2009;Domagała et al, 2012), as performed here for the ELMAM2 model of HEWL. Apparently, this feature has been overlooked in previous electron-density studies on proteins, in which at least part of the multipole parameters have been refined Schmidt et al, 2003Schmidt et al, , 2011Guillot et al, 2008).…”

Temperature-dependent analysis of thermal motion, disorder and structures of tris(ethylenediamine)zinc(II) sulfate and tris(ethylenediamine)copper(II) sulfate

“…The indication for a temperature-independent contribution to the ADPs is thus still present, if less significant. The difference may be attributed to the fact that for low-resolution data ADPs are more influenced by the non-spherical valence electron density than for high-resolution data (Dittrich et al, 2008). Temperature-independent contributions of this magnitude are usually associated with unresolved positional disorder of the affected atoms (Bü rgi & Capelli, 2003), as will be discussed in more detail in xx4.2 and 4.3.…”