ACORN: a review

Abstract

The ACORN system was originally developed as a means of ab initio solution of protein structures when atomic resolution data were available. The first step is to obtain a starting set of phases, which must be at least slightly better than random. These may be calculated from a fragment of the structure, which can be anything from a single metal atom to a complete molecular-replacement model. A number of standard procedures are available in ACORN to orientate and position such a fragment. The fragment provides initial phases that give the first of a series of maps that are iteratively refined by a dynamic density-modification (DDM) process. Another FFTbased procedure is Sayre-equation refinement (SER), which modifies phases better to satisfy the Sayre equation. With good-quality atomic resolution data, the final outcome of applying DDM and SER is a map similar in appearance to that found from a refined structure, which is readily interpreted by automated procedures. Further development of ACORN now enables structures to be solved with less than atomic resolution data. A critical part of this development is the artificial extension of the data from the observed limit to 1 Å resolution. These extended reflections are allocated unit normalized structure amplitudes and then treated in a similar way to observed reflections except that they are downweighted in the calculation of maps. ACORN maps, especially at low resolution, tend to show C atoms less well, in particular C atoms which fall within the first diffraction minimum of their three neighbours. Two new density-modification procedures (DDM1 and DDM2) and a density-enhancement procedure (ENH) have been devised to counter this problem. It is demonstrated that high-quality maps showing individual atoms can be produced with the new ACORN. ACORN has also been demonstrated to be very effective in refining phase sets derived from physical processes such as those using anomalous scattering or isomorphous derivative data. Future work will be directed towards applying ACORN to resolutions down to 2 Å .

N15 Cro and λ Cro: Orthologous DNA‐binding domains with completely different but equally effective homodimer interfaces

“…The data were reduced and scaled using CrystalClear (d*trek) (Pflugrath 1999). Due to the high resolution of the data, the phase problem was solvable by the program ACORN (Yao et al 2006) using as a seed structure an idealized 10‐residue polyalanine α‐helix. The seed structure was placed in the cell using rotation and translation functions; the top solution had a correlation coefficient (CC) of 0.054.…”

The Crystal Structure of Non‐Modified and Bipyridine‐Modified PNA Duplexes

“…This data set was independently solved by using SHELXS [47] to identify the 50 strongest peaks as starting coordinates for the less flexible PNA peptide backbone atoms to be used in ACORN. [48] The 8-bp PNA structure was refined following the same protocols as described above for the bipy PNA. The model contains four PNA strandsagain related by a pseudo-inversion center.…”

Structures of viscotoxins A1 and B2 from European mistletoe solved using native data alone

“…with the peak-list optimization, density modification with SHELXE was applied starting from the S atoms located by SHELXD; this is similar to the way in which the program ACORN can be used to solve structures starting from a few heavier atoms such as sulfur (Yao et al, 2006). This resulted in a very clear high-quality map shown in Fig.…”