ACHESYM: an algorithm and server for standardized placement of macromolecular models in the unit cell

Abstract

Despite the existence of numerous useful conventions in structural crystallography, for example for the choice of the asymmetric part of the unit cell or of reciprocal space, surprisingly no standards are in use for the placement of the molecular model in the unit cell, often leading to inconsistencies or confusion. A conceptual solution for this problem has been proposed for macromolecular crystal structures based on the idea of the anti-Cheshire unit cell. Here, a program and server (called ACHESYM; http://achesym.ibch.poznan.pl) are presented for the practical implementation of this concept. In addition, the first task of ACHESYM is to find an optimal (compact) macromolecular assembly if more than one polymer chain exists. ACHESYM processes PDB (atomic parameters and TLS matrices) and mmCIF (diffraction data) input files to produce a new coordinate set and to reindex the reflections and modify their phases, if necessary.

Substrate specificity and reaction mechanism of human prolidase

“…The diffraction data precision index (DPI) was calculated using the web server run by Kumar et al [68]. The program ACHESYM [69] was used to find the best origin of the unit cell and place a model. The presence of Mn 2+ ions was confirmed by examining anomalous difference maps obtained from anomalous differences resulting from the long-wavelength data sets with the use of program ANODE [70].…”

Structural Studies of Medicago truncatula Histidinol Phosphate Phosphatase from Inositol Monophosphatase Superfamily Reveal Details of Penultimate Step of Histidine Biosynthesis in Plants

“…Automatic model building was carried out with the on-line version of ARP/ wARP (34). The atomic coordinates were placed inside the unit cell with ACHESYM server (35). COOT (36) was used for manual fitting in the electron density maps between rounds of model refinement in Refmac (37).…”

Recognition of the Major Histocompatibility Complex (MHC) Class Ib Molecule H2-Q10 by the Natural Killer Cell Receptor Ly49C

“…The asymmetric unit comprised two molecules of H2-Q10 VGI and two Ly49C monomers. The contents of the asymmetric unit were reorganized using the ACHESYM algorithm (41), revealing that the Ly49C monomers formed a dimer. Thus, the entire complex was composed of one Ly49C dimer and two molecules of H2-Q10…”