X-ray crystallographic studies of RoAb13 bound to PIYDIN, a part of the N-terminal domain of C-C chemokine receptor 5

C-C chemokine receptor 5 (CCR5) is a major co-receptor molecule used by HIV-1 to enter cells. This led to the hypothesis that stimulating an antibody response would block HIV with minimal toxicity. Here, X-ray crystallographic studies of the anti-CCR5 antibody RoAb13 together with two peptides were undertaken: one peptide is a 31-residue peptide containing the PIYDIN sequence and the other is the PIDYIN peptide alone, where PIYDIN is part of the N-terminal region of CCR5 previously shown to be important for HIV entry. In the presence of the longer peptide (the complete N-terminal domain), difference electron density was observed at a site within a hypervariable CDR3 binding region. In the presence of the shorter core peptide PIYDIN, difference electron density is again observed at this CDR3 site, confirming consistent binding for both peptides. This may be useful in the design of a new biomimetic to stimulate an antibody response to CCR5 in order to block HIV infection.

Mismodeled purines: implicit alternates and hidden Hoogsteens

Hoogsteen base pairs are seen in DNA crystal structures, but only rarely. This study tests whether Hoogsteens or othersynpurines are either under-modeled or over-modeled, which are known problems for rare conformations. Candidate purines needing asyn/anti180° flip were identified by diagnostic patterns of difference electron-density peaks. Manual inspection narrowed 105 flip candidates to 20 convincing cases, all at ≤2.7 Å resolution. Rebuilding and refinement confirmed that 14 of these were authentic purine flips. Seven examples are modeled as Watson–Crick base pairs but should be Hoogsteens (commonest at duplex termini), and three had the opposite issue.Syn/antiflips were also needed for some single-stranded purines. Five of the 20 convincing cases arose from an unmodeled alternate duplex running in the opposite direction. These are in semi-palindromic DNA sequences bound by a homodimeric protein and show flipped-purine-like difference peaks at residues where the palindrome is imperfect. This study documents types of incorrect modeling which are worth avoiding. However, the primary conclusions are that such mistakes are infrequent, the bias towards fittingantipurines is very slight, and the occurrence rate of Hoogsteen base pairs in DNA crystal structures remains unchanged from earlier estimates at ∼0.3%.

Deducing fast electron density changes in randomly orientated uncrystallized biomolecules in a pump–probe experiment

We propose a method for deducing time-resolved structural changes in uncrystallized biomolecules in solution. The method relies on measuring the angular correlations of the intensities, when averaged over a large number of diffraction patterns from randomly oriented biomolecules in solution in a liquid solvent. The experiment is somewhat like a pump–probe version of an experiment on small angle X-ray scattering, except that the data expected by the algorithm are not just the radial variation of the averaged intensities. The differences of these correlation functions as measured from a photoexcited and dark structure enable the direct calculation of the difference electron density with a knowledge of only the dark structure. We exploit a linear relation we derive between the difference in these correlation functions and the difference electron density, applicable for small structural changes.

Electronic and phononic properties of V2AlC via first principles

The electronic and phononic properties of V2AlC have been extensively studied using ab initio pseudopotential density functional theory. Our investigations revealed that the longest V–V bond and its least variations have led to the stiffer c axis. The nearly unchanged net charge of the C atom under pressure has led to nearly unchanged overlapped populations along the C–V bond. The obvious charge transfer of V → Al has induced significant variations of the overlapped populations along Al–V and V–V bonds. An anomalous variation of charge transfer between V and Al atoms and V–V bond populations at about 700 GPa has been revealed, which may relate to its structural instability at about 731 GPa. Previously calculated structural instability at about 731 GPa has been successfully confirmed by the present phonon dispersion curve. The bonding natures are also studied by the electron density difference, electron density of states, and the energy band structure.

(Acetylacetonato-κ2O,O′)[(2-bromophenyl)diphenylphosphane-κP]carbonylrhodium(I)

In the title compound, [Rh(C5H7O2)(C18H14BrP)(CO)], the RhIatom adopts a slightly distorted square-planar geometry involving two O atoms [Rh—O = 2.077 (2) and 2.033 (2) Å] of the acetylacetonate ligand, one carbonyl C atom [Rh—C = 1.813 (2) Å] and one P atom [Rh—P = 2.242 (5) Å] of the PPh2(2-BrC6H4) phosphane ligand. Difference electron density maps indicate a disorder of the Br atom over two positions in an approximate 0.95:0.05 ratio. However, this disorder could not be resolved satisfactorily with the present data.

From a random to the correct structure: the VLD algorithm

A recent probabilistic reformulation of the difference electron-density Fourier synthesis [Burla, Caliandro, Giacovazzo & Polidori (2010).Acta Cryst.A66, 347–361] suggested that the most suitable Fourier coefficients are the sum of the classical difference term (mF−DFp) with a flipping term, depending on the model and on its quality. The flipping term is dominant when the model is poor and is negligible when the model is a good representation of the target structure. In the case of a random model the Fourier coefficient does not vanish and therefore could allow the recovery of the target structure from a random model. This paper describes a new phasing algorithm which does not require use of the concept of structure invariants or semi-invariants: it is based only on the properties of the new difference electron density and of the observed Fourier synthesis. The algorithm is cyclic and very easy to implement. It has been applied to a large set of small-molecule structures to verify the suitability of the approach.