Open AccessApplications of ACORN to data at 1.45 Å resolution
Author(s) -
Rajakannan V.,
Yamane T.,
Shirai T.,
Kobayashi T.,
Ito S.,
Velmurugan D.
Publication year - 2003
Publication title -
journal of synchrotron radiation
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.172
H-Index - 99
ISSN - 1600-5775
DOI - 10.1107/s0909049503023537
Subject(s) - phaser , acorn , data structure , resolution (logic) , computer science , protein data bank (rcsb pdb) , function (biology) , crystallography , algorithm , data mining , chemistry , physics , programming language , biology , stereochemistry , optics , ecology , evolutionary biology
One of the main interests in the molecular biosciences is in understanding structure–function relations and X‐ray crystallography plays a major role in this. ACORN can be used as a comprehensive and efficient phasing procedure for the determination of protein structures when atomic resolution data are available. An initial model can automatically be built by ARP/wARP followed by REFMAC for refinement. The α helices and β sheets occurring in many protein structures can be taken as starting fragments for structure solution in ACORN. ACORN, along with ARP/wARP followed by REFMAC, can be an ab initio method for solving protein structure for which data are better than 1.2 Å (atomic resolution). Attempts are here made in extending its applications to real data at 1.45 Å resolution and also to truncated data at 1.6 Å resolution. Two previously known structures, congerin II and alkaline cellulase N257, were resolved using the above approach. Automatic structure solution, phasing and refinement for real data at still lower resolutions for proteins of various complexities are being carried out. Data mining of the secondary structural features using PDB is being carried out for this new approach for `seed‐phasing' to ACORN.