A robust tangent procedure

MPF, a multipurpose figure of merit for phasing procedures

The efficient multipurpose figure of merit MPF has been defined and characterized. It may be very helpful in phasing procedures. Indeed, it might be used for establishing the centric or acentric nature of an unknown structure, for identifying the presence of some pseudotranslational symmetry, for recognizing the correct solution in multisolution approaches and for estimating the quality of structure models as they become available during the phasing process. Thus, phase improvement or deterioration may be monitored and useless models may be discarded to save computing time. It is also shown that MPF may be applied in different phasing approaches, no matter ifab initioor nonab initio.

Direct-methods structure determination of a trypanosome RNA-editing substrate fragment with translational pseudosymmetry

Using direct methods starting from random phases, the crystal structure of a 32-base-pair RNA (675 non-H RNA atoms in the asymmetric unit) was determined using only the native diffraction data (resolution limit 1.05 Å) and the computer program SIR2014. The almost three helical turns of the RNA in the asymmetric unit introduced partial or imperfect translational pseudosymmetry (TPS) that modulated the intensities when averaged by the l Miller indices but still escaped automated detection. Almost six times as many random phase sets had to be tested on average to reach a correct structure compared with a similar-sized RNA hairpin (27 nucleotides, 580 non-H RNA atoms) without TPS. More sensitive methods are needed for the automated detection of partial TPS.

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.

An alternative method for the calculation of joint probability distributions. Application to the expectation of the triplet invariant

This paper presents a completely new method for the calculation of expectations (and thus joint probability distributions) of structure factors or phase invariants. As an example, a first approximation of the expectation of the triplet invariant (up to a constant) is given and acomplexnumber is obtained. Instead of considering the atomic vector positions or reciprocal vectors as the fundamental random variables, the method samples over all functions (distributions) with a given number of atoms and given Patterson function. The aim of this paper was to explore the feasibility of the method, so the easiest problem was chosen: the calculation of the expectation value of the triplet invariant inP1. Calculation of the jointprobabilitydistribution of the triplet is not performed here but will be done in the future.

SHELXT - integrated space-group and crystal-structure determination

The new computer program SHELXT employs a novel dual-space algorithm to solve the phase problem for single-crystal reflection data expanded to the space group P1. Missing data are taken into account and the resolution extended if necessary. All space groups in the specified Laue group are tested to find which are consistent with the P1 phases. After applying the resulting origin shifts and space-group symmetry, the solutions are subject to further dual-space recycling followed by a peak search and summation of the electron density around each peak. Elements are assigned to give the best fit to the integrated peak densities and if necessary additional elements are considered. An isotropic refinement is followed for non-centrosymmetric space groups by the calculation of a Flack parameter and, if appropriate, inversion of the structure. The structure is assembled to maximize its connectivity and centred optimally in the unit cell. SHELXT has already solved many thousand structures with a high success rate, and is optimized for multiprocessor computers. It is, however, unsuitable for severely disordered and twinned structures because it is based on the assumption that the structure consists of atoms.

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

Phasing proteins at non-atomic resolution is still a challenge for any ab initio method. A variety of algorithms [Patterson deconvolution, superposition techniques, a cross-correlation function (C map), the VLD (vive la difference) approach, the FF function, a nonlinear iterative peak-clipping algorithm (SNIP) for defining the background of a map and the free lunch extrapolation method] have been combined to overcome the lack of experimental information at non-atomic resolution. The method has been applied to a large number of protein diffraction data sets with resolutions varying from atomic to 2.1 Å, with the condition that S or heavier atoms are present in the protein structure. The applications include the use of ARP/wARP to check the quality of the final electron-density maps in an objective way. The results show that resolution is still the maximum obstacle to protein phasing, but also suggest that the solution of protein structures at 2.1 Å resolution is a feasible, even if still an exceptional, task for the combined set of algorithms implemented in the phasing program. The approach described here is more efficient than the previously described procedures: e.g. the combined use of the algorithms mentioned above is frequently able to provide phases of sufficiently high quality to allow automatic model building. The method is implemented in the current version of SIR2014.