A quick solution: ab initio structure determination of a 19 kDa metalloproteinase using ACORN.

A data set from the metalloproteinase deuterolysin was collected at atomic resolution (1.0 A) with synchrotron radiation. The high resolution allowed the structure to be solved with the new direct-methods program ACORN using the coordinates of the Zn atom as a starting point. The phases obtained from ACORN were of sufficient quality to allow automated building to be carried out in ARP/wARP. Minimal manual rebuilding of the model was required and the structure determination was completed using the maximum-likelihood refinement program REFMAC. The whole process, starting from the processed and merged data and ending with a refined model, required less than 6 h of computational time.

A flexible and efficient procedure for the solution and phase refinement of protein structures.

An ab initio method is described for solving protein structures for which atomic resolution (better than 1.2 A) data are available. The problem is divided into two stages. Firstly, a substructure composed of a small percentage ( approximately 5%) of the scattering matter of the unit cell is positioned. This is used to generate a starting set of phases that are slightly better than random. Secondly, the full structure is developed from this phase set. The substructure can be a constellation of atoms that scatter anomalously, such as metal or S atoms. Alternatively, a structural fragment such as an idealized alpha-helix or a motif from some distantly related protein can be orientated and sometimes positioned by an extensive molecular-replacement search, checking the correlation coefficient between observed and calculated structure factors for the highest normalized structure-factor amplitudes |E|. The top solutions are further ranked on the correlation coefficient for all E values. The phases generated from such fragments are improved using Patterson superposition maps and Sayre-equation refinement carried out with fast Fourier transforms. Phase refinement is completed using a novel density-modification process referred to as dynamic density modification (DDM). The method is illustrated by the solution of a number of known proteins. It has proved fast and very effective, able in these tests to solve proteins of up to 5000 atoms. The resulting electron-density maps show the major part of the structures at atomic resolution and can readily be interpreted by automated procedures.

New techniques for applying anomalous-scattering and isomorphous-replacement data incorporated in ANOMIR - a general application package.

A computer package ANOMIR is described which can derive phases from anomalous scattering and/or isomorphous-replacement data in any combination. For anomalous scattering it incorporates five methods of applying one-wavelength data and three methods for multiple-wavelength data including SPIN, reported here for the first time. In addition there are three procedures for multiple-wavelength data - the first modifying data for different wavelengths to make them mutually consistent, the second estimating the contributions of the anomalous scatterers alone and the third which finds anomalous differences. For single isomorphous replacement or one-wavelength anomalous scattering the phase ambiguity can be resolved by the direct method [Fan, Han, Qian & Yao (1984). Acta Cryst. A40, 489- 495] but for multiple isomorphous replacement the main method is an adaptation of the probability-curve method [Blow & Crick (1959). Acta Cryst. 12, 794-802]. A new statistical method is described for estimating the standard error in measuring magnitudes which is independent of having subsets of centric reflections. A method is described whereby the weights associated with phase estimates are used to generate probability curves, through which it is possible to combine estimates from different methods and to produce a 'best phase' and figure-of-merit for every reflection. ANOMIR procedures are also available for handling combinations of one-wavelength anomalous scattering with single- or multiple-isomorphous replacement. A final process, which is always beneficial, is a single parallel application of the tangent formula. The ANOMIR package has been designed for easy use and is controlled throughout by KEYWORDS. Results for several structures are given and compared with those found from the MLPHARE program in the CCP4 package.