ACORN — theory and practice

Abstract

ACORN is a flexible and general procedure for the ab initio solution of protein structures when atomic resolution data are available. It has two components — ACORN-MR that locates a single atom or a fragment of the structure and ACORN-PHASE that refines the structure starting with the phase estimates from the fragment. ACORN-MR depends heavily on a correlation coefficient (CC) between the observed normalized structure factors and those from the fragment to find the fragment‘s correct orientation and/or position. ACORN-PHASE has three components, a Patterson-superposition sum function, real-space Sayre-equation refinement and, most importantly, Dynamic Density Modification (DDM). The concepts that underline DDM are explained by a theoretical approach. ACORN has been shown in trials to be able to solve structures with up to 5000 independent non-hydrogen atoms in the asymmetric unit. Several previously unknown structures have also been solved. At lower resolution, if anomalous scattering or isomorphous replacement data are available, then substructures can be determined using the ACORN approach. The quality of the final maps from ACORN, without further processing, enables automatic interpretation in terms of structure to be readily made.