Protein phasing at non-atomic resolution by combining Patterson and VLD techniques

SEQUENCE SLIDER: expanding polyalanine fragments for phasing with multiple side-chain hypotheses

Fragment-based molecular-replacement methods can solve a macromolecular structure quasi-ab initio. ARCIMBOLDO, using a common secondary-structure or tertiary-structure template or a library of folds, locates these with Phaser and reveals the rest of the structure by density modification and autotracing in SHELXE. The latter stage is challenging when dealing with diffraction data at lower resolution, low solvent content, high β-sheet composition or situations in which the initial fragments represent a low fraction of the total scattering or where their accuracy is low. SEQUENCE SLIDER aims to overcome these complications by extending the initial polyalanine fragment with side chains in a multisolution framework. Its use is illustrated on test cases and previously unknown structures. The selection and order of fragments to be extended follows the decrease in log-likelihood gain (LLG) calculated with Phaser upon the omission of each single fragment. When the starting substructure is derived from a remote homolog, sequence assignment to fragments is restricted by the original alignment. Otherwise, the secondary-structure prediction is matched to that found in fragments and traces. Sequence hypotheses are trialled in a brute-force approach through side-chain building and refinement. Scoring the refined models through their LLG in Phaser may allow discrimination of the correct sequence or filter the best partial structures for further density modification and autotracing. The default limits for the number of models to pursue are hardware dependent. In its most economic implementation, suitable for a single laptop, the main-chain trace is extended as polyserine rather than trialling models with different sequence assignments, which requires a grid or multicore machine. SEQUENCE SLIDER has been instrumental in solving two novel structures: that of MltC from 2.7 Å resolution data and that of a pneumococcal lipoprotein with 638 residues and 35% solvent content.

Synergy among phase-refinement techniques in macromolecular crystallography

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.

Solving proteins at non-atomic resolution by direct methods: update

Direct methods can be used to solve proteins of great structural complexity even when diffraction data are at non-atomic resolution. However, one of the main obstacles to the wider application of direct methods is that they reliably phase only a small fraction of the observed reflections, those with a sufficiently large value of the normalized structure factor amplitude. The subsequent phase expansion and refinement required for full structure solution are difficult. Here a new phase refinement procedure is described, which combines (1–2) difference Fourier synthesis with electron density modification techniques and thevive la differenceand Free Lunch algorithms. This procedure is able to solve data resistant to other direct space refinement procedures.

Residue-based scattering factors

A glob is defined as a group of atoms in the crystal which can be chosen in various ways. Globs themselves can be used as scattering elements in the theory of structure determination, just as atoms are used at present. In this paper, amino-acid residues are chosen to form globs and empirical formulas for residue-based scattering factors have been developed.

Phase improvementviathePhantom Derivativetechnique: ancils that are related to the target structure

Density modification is a general standard technique which may be used to improve electron density derived from experimental phasing and also to refine densities obtained byab initioapproaches. Here, a novel method to expand density modification is presented, termed thePhantom derivativetechnique, which is based on non-existent structure factors and is of particular interest in molecular replacement. ThePhantom derivativeapproach uses randomly generated ancil structures with the same unit cell as the target structure to create non-existent derivatives of the target structure, called phantom derivatives, which may be used forab initiophasing or for refining the available target structure model. In this paper, it is supposed that a model electron density is available: it is shown that ancil structures related to the target obtained by shifting the target by origin-permissible translations may be employed to refine model phases. The method enlarges the concept of the ancil, is as efficient as the canonical approach using random ancils and significantly reduces the CPU refinement time. The results from many real test cases show that the proposed methods can substantially improve the quality of electron-density maps from molecular-replacement-based phases.

Refining a model electron-density mapviathePhantom Derivativemethod

ThePhantom Derivative(PhD) method [Giacovazzo (2015),Acta Cryst.A71, 483–512] has recently been described forab initioand non-ab initiophasing. It is based on the random generation of structures with the same unit cell and the same space group as the target structure (called ancil structures), which are used to create derivatives devoid of experimental diffraction amplitudes. In this paper, the non-ab initiovariant of the method was checked using phase sets obtained by molecular-replacement techniques as a starting point for phase extension and refinement. It has been shown that application ofPhDis able to extend and refine phases in a way that is competitive with other electron-density modification techniques.

Solution of the phase problem at non-atomic resolution by the phantom derivative method

For a given unknown crystal structure (thetarget),nrandom structures, arbitrarily designed without any care for their chemical consistency and usually uncorrelated with the target, are sheltered in the same unit cell as the target structure and submitted to the same space-group symmetry. (These are called ancil structures.) The composite structures, whose electron densities are the sum of the target and of the ancil electron densities, are denotedderivatives. No observed diffraction amplitudes are available for them: in order to emphasize their unreal nature, the termphantomis added. The paper describes the theoretical basis by which the phantom derivative method may be used to phase the target structure. It may be guessed that 100–300 ancil structures may be sufficient for phasing a target structure, so that the phasing technique may be denoted as the multiple phantom derivative method. Ancil phases and amplitudes may be initially combined with observed target magnitudes to estimate amplitudes and phases of the corresponding phantom derivative. From them suitable algorithms allow one to obtain poor target phase estimates, which are often improved by combining the indications arising from each derivative. Probabilistic criteria are described to recognize the most reliable target phase estimates. The method is cyclic: the target phase estimates just obtained are used to improve amplitudes and phases of each derivative, which, in their turn, are employed to provide better target phase estimates. The method is a fullyab initiomethod, because it needs only the experimental data of the target structure. The term derivative is maintained with reference to SIR–MIR (single isomorphous replacement–multiple isomorphous replacement) techniques, even if its meaning is different: therefore the reader should think of the phantom derivative method more as a new method than as a variant of SIR–MIR techniques. The differences are much greater than the analogies. The paper also describes how phantom derivatives may be used for improving structure models obtainedviaotherab initioor non-ab initiotechniques. The method is expected to be insensitive to the structural complexity of the target and to the target experimental data resolution, provided it is better than 4–6 Å.

Crystal structure determination and refinementviaSIR2014

SIR2014is the latest program of theSIRsuite for crystal structure solution of small, medium and large structures. A variety of phasing algorithms have been implemented, bothab initio(standard or modern direct methods, Patterson techniques,Vive la Différence) and non-ab initio(simulated annealing, molecular replacement). The program contains tools for crystal structure refinement and for the study of three-dimensional electron-density mapsviasuitable viewers.