Synergy among phase-refinement techniques in macromolecular crystallography

Abstract

Ab initio and non-ab initio phasing methods are often unable to provide phases of sufficient quality to allow the molecular interpretation of the resulting electron-density maps. Phase extension and refinement is therefore a necessary step: its success or failure can make the difference between solution and nonsolution of the crystal structure. Today phase refinement is trusted to electron-density modification (EDM) techniques, and in practice to dual-space methods which try, via suitable constraints in direct and in reciprocal space, to generate higher quality electron-density maps. The most popular EDM approaches, denoted here as mainstream methods, are usually part of packages which assist crystallographers in all of the structure-solution steps from initial phasing to the point where the molecular model perfectly fits the known features of protein chemistry. Other phase-refinement approaches that are based on different sources of information, denoted here as out-of-mainstream methods, are not frequently employed. This paper aims to show that mainstream and out-of-mainstream methods may be combined and may lead to dramatic advances in the present state of the art. The statement is confirmed by experimental tests using molecular-replacement, SAD-MAD and ab initio techniques.

How far are we from automatic crystal structure solution via molecular-replacement techniques?

“…We used 80 protein and 38 nucleic acid test structures, the PDB codes of which are reported in Tables 1 and 2. The first 34 protein test structures had previously been used by Burla et al (2017) to check the SYNERGY refinement process on standard REMO09 phases. Proteins 25-34 belong to the set of 13 structures studied by DiMaio et al (2011) and characterized by an SI between the model and target structures of lower than 0.30.…”

“…Joint distributions were also derived for the translation step: a monomer is located given its own orientation or the orientations and/or locations of other monomers. Burla et al (2017), starting from REMO09 phases, checked the efficiency of a phase-refinement pipeline which synergically combines mainstream refinement techniques (specifically DM; Cowtan, 2001) with out-of-mainstream techniques [specifically, free lunch (Caliandro et al, 2005a,b), low-density Fourier transform (Giacovazzo & Siliqi, 1997), vive la difference (Burla, Caliandro et al, 2010;, Phantom derivative (Giacovazzo, 2015b;Carrozzini et al, 2016) and phase-driven model refinement (Giacovazzo, 2015a)]. For simplicity, we will refer to this modulus as SYNERGY.…”

“…For simplicity, we will refer to this modulus as SYNERGY. Burla et al (2017) automatically submitted the protein data obtained by SYNERGY to the AMB procedure CAB (Burla et al, 2017): it applies Buccaneer (Cowtan, 2006) in a cyclic way.…”

Cyclic Automated Model Building (CAB) Applied to Nucleic Acids

“…We suppose that a set of observed structure factor amplitudes with refined φ r phases and w r weights are available as the starting point for any AMB application. They were first obtained by applying REMO09 [14] to the test structures, and then refined via the SYNERGY approach [15]. The name of the latter procedure arises from the fact that it combines mainstream phase refinement procedures (DM by Cowtan [16]) and out-of-mainstream phase refinement techniques.…”

CAB: a cyclic automatic model-building procedure

“…CAB has been tested on 81 protein structures that were solved via molecularreplacement, anomalous dispersion and ab initio methods. The corresponding phases were submitted to a phase-refinement process that synergically combines current phase-refinement techniques and out-of-mainstream refinement methods [Burla et al (2017), Acta Cryst. D73, [877][878][879][880][881][882][883][884][885][886][887][888].…”