Updated restraint dictionaries for carbohydrates in the pyranose form.

Mihaela Atanasova,Robbie P. Joosten,Jon Agirre,Robert A. Nicholls

doi:10.1107/s2059798322001103

Abstract

Restraint dictionaries are used during macromolecular structure refinement to encapsulate intramolecular connectivity and geometric information. These dictionaries allow previously determined `ideal' values of features such as bond lengths, angles and torsions to be used as restraint targets. During refinement, restraints influence the model to adopt a conformation that agrees with prior observation. This is especially important when refining crystal structures of glycosylated proteins, as their resolutions tend to be worse than those of nonglycosylated proteins. Pyranosides, the overwhelming majority component in all forms of protein glycosylation, often display conformational errors in crystal structures. Whilst many of these flaws usually relate to model building, refinement issues may also have their root in suboptimal restraint dictionaries. In order to avoid subsequent misinterpretation and to improve the quality of allpyranose monosaccharide entries in the CCP4 Monomer Library, new dictionaries with improved ring torsion restraints, coordinates reflecting the lowest-energy ring pucker and updated geometry have been produced and evaluated. These new dictionaries are now part of the CCP4 Monomer Library and will be released with CCP4 version 8.0.

Highlights

The restraint dictionary entries that are used by the software in the CCP4 suite (Winn et al, 2011) are collected in the CCP4 Monomer Library (Vagin et al, 2004)
A set of 243 new carbohydrate dictionaries has been produced with updated torsion restraints that encourage refinement software to retain the minimal energy ring pucker
As expected, introducing additional restraints, in this case the torsional kind, may occasionally lead to a lower real-space correlation coefficient (RSCC) between the model and map. This reflects the fact that the refinement software is no longer able to improve the model-to-map correlation at the expense of stereochemical geometry, for example unfavourable bond lengths or angles or inverted ring conformations that would require a massive expenditure of energy

Summary

Introduction

Macromolecular refinement is a computational procedure that lies among the final steps in protein structure solution. Due to limited data resolution, prior chemical knowledge about the molecules involved is usually required in order to maintain refinement stability. In macromolecular crystallography, such prior knowledge is stored in dictionaries, typically in the form of Crystallographic Information Files (CIFs; Hall et al, 1991; Brown & McMahon, 2002) or MOL(2) files (MDL Information Systems, San Leandro, California, USA). The restraint dictionary entries that are used by the software in the CCP4 suite (Winn et al, 2011) are collected in the CCP4 Monomer Library (Vagin et al, 2004) Such prior chemical knowledge usually consists of atom names, a description of stereochemical properties such as connectivity, bond lengths, angles, chirality, torsion angles and, if applicable, a list of groups of four or more atoms in planar co-arrangements

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