ACORN in CCP4 and its applications

Abstract

ACORN is a comprehensive and ef®cient phasing procedure for the determination of protein structures when atomic resolution data are available. Reliable phases can be developed from a fragment composed of a small percentage (less than 5%) of the scattering matter of the unit cell. For example, ACORN has been used to solve a structure of 1093 atoms from only one S atom. The map from ACORN typically reveals the 90% of whole structure. The initial model can be automatically built using ARP/wARP or QUANTA. ACORN can also be used to determine substructures of heavy atoms or anomalously scattering atoms from SAD or MAD data at much lower resolutions such as 3.5 A Ê . Some test results of using ACORN on known structures are presented here. ACORN has solved four new protein structures by users in the UK and France, and some results kindly provided by them are described in this paper.

Experimental phasing with SHELXC/D/E: combining chain tracing with density modification

“…For voxels with high V, is replaced by [ 4 /( 2 2 () + 2 )] 1/2 [with usually 0.5 and where 2 () is the variance of the density over the whole cell] if positive and by zero if negative. This has a similar effect to the procedure used in the CCP4 program ACORN (Yao, 2002), which however applies the same procedure to all voxels. For intermediate values of V a suitably weighted mixture of the two treatments is used.…”

Crystal Structure of the ENT Domain of Human EMSY

“…5 The crystal structure was solved to 1.1 Å resolution using ab initio phasing methods with the program ACORN. 6 Secondary structure predictions using the sequence of the ENT domain suggested that it was composed predominantly of a-helices. Therefore, the ACORN-MR option was used to generate normalized structure factors from the observed data and model.…”

“…6 Phases were determined for the 1.1 Å data by using a 15 residue helical fragment from the CCP4 fragment library and applied to the program ACORN-MR to produce an interpretable electron density map. An atomic model was built into this phased map by docking the sequence of the protein.…”

Ab initio phasing of a nucleoside hydrolase‐related hypothetical protein from Saccharophagus degradans that is associated with carbohydrate metabolism

“…These were assumed to be primarily the sulphur atoms present in the 11 methionines and four cysteines in the crystallized protein. The determination of phases was ultimately achieved by using the set of 16 atoms located with the low energy data set as a seed atom set for ab initio phasing of the 1.08 Å resolution data and the program ACORN 17. This resulted in an outstanding set of phases that allowed rapid automated model building of a complete model [Fig.…”