Validation of crystallographic models containing TLS or other descriptions of anisotropy

Abstract

The use of TLS (translation/libration/screw) models to describe anisotropic displacement of atoms within a protein crystal structure has become increasingly common. These models may be used purely as an improved methodology for crystallographic refinement or as the basis for analyzing inter-domain and other large-scale motions implied by the crystal structure. In either case it is desirable to validate that the crystallographic model, including the TLS description of anisotropy, conforms to our best understanding of protein structures and their modes of flexibility. A set of validation tests has been implemented that can be integrated into ongoing crystallographic refinement or run afterwards to evaluate a previously refined structure. In either case validation can serve to increase confidence that the model is correct, to highlight aspects of the model that may be improved or to strengthen the evidence supporting specific modes of flexibility inferred from the refined TLS model. Automated validation checks have been added to the PARVATI and TLSMD web servers and incorporated into the CCP4i user interface.

Structural Basis for the Recognition of Peptide RJPXD33 by Acyltransferases in Lipid A Biosynthesis

“…Iterative rounds of refinement and model building were completed using Buster (18) and Coot (19). MolProbity (20,21) and Parvarti (22) were used to validate the structures. Figures were generated in PyMOL 1.7.0.3 (Schrödinger LLC) in which pairwise structural alignments were generated using align or cealign.…”

Crystal structure and RNA-binding properties of an Hfq homolog from the deep-branching Aquificae: Conservation of the lateral RNA-binding mode

“…The P1 and P6 data sets contained 16.5 and 17.5 reflections per atom, respectively, making the anisotropic refinement problem nearly twofold overdetermined; the unsupervised decision algorithm in PDB_REDO identified a fully anisotropic, individual B-factor model as being optimal. The structural models resulting from various ADP refinement strategies were assessed using the protein anisotropic refinement validation and analysis tool PARVATI (Zucker et al, 2010). In the final refinement stages for both Aae Hfq crystal forms, P1 (Z = 12) and P6 (Z = 6), full anisotropic B-factor tensors were refined individually for virtually every atom.…”

SomeBeqare more equivalent than others

“…For an isotropic atom, A = 1. The mean anisotropy of atoms in individual macromolecular crystal structures refined at atomic resolution lies broadly in the range 0.4-0.6, with atoms in the structure exhibiting a roughly Gaussian distribution about that mean (Zucker et al, 2010). Estimates for B iso made using B est rather than B eq will therefore be significantly smaller for most atoms in such structures.…”

“…This is borne out experimentally both by refinement of anisotropic ADPs for the small fraction of protein structures that diffract to true atomic resolution (Schneider, 1996;Merritt, 1999b) and by the improved R-factors obtained even for low-resolution structures when relatively simple descriptions of bulk anisotropy are added to the model (Merritt, 2011). Thus it is becoming standard practice in protein crystallography to include an explicit model for bulk anisotropic displacements (Zucker et al, 2010). The most common approach is to treat segments of the protein as approximately rigid groups exhibiting concerted displacements described by the translation/libration/screw (TLS) formalism (Trueblood, 1978;Howlin et al, 1989;Winn et al, 2001;Painter & Merritt, 2006).…”