Use of the rotation and translation functions

Lattman, Eaton E.

doi:10.1016/0076-6879(85)15007-x

Cited by 48 publications

(19 citation statements)

References 13 publications

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“…The choice of PC (12) is related to the product function <lFob~l~lF. (n)l~) which is often used in conventional MR (Lattman, 1985). However, in conventional MR the structure factors F,, are computed in a large orthorhombic P~ box.…”

Section: Pc Refinementmentioning

confidence: 99%

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Extension of molecular replacement: a new search strategy based on Patterson correlation refinement

Brünger¹

1990

Acta Cryst Sect A

313

118

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A new search strategy is presented to obtain initial phases for single-crystal diffraction data by molecular replacement. It consists of carrying out 'Patterson refinements' of a large number of the highest peaks of a rotation function. The target function for Patterson refinement is proportional to the negative correlation coefficient between the squared amplitudes of the observed and the calculated normalized structure factors. If the root-mean-square difference between the search model and the crystal structure is within the radius of convergence of the minimization procedure employed, the correct orientation can be identified by having the lowest value of the target function after refinement. Similar to conventional crystallographic R-factor refinement, the target function for Patterson refinement may be combined with an empirical energy function describing geometric and non-bonded interactions. Patterson refinement of individual atomic coordinates or of rigid-group parameters may be carried out. Search models of crambin and of myoglobin with 1.6-2.0/~ backbone atomic r.m.s, differences from the target crystal structures show that the Patterson refinement strategy can solve crystal structures that cannot be solved by conventional molecular replacement or even by full six-dimensional searches. Abbreviations

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Section: Pc Refinementmentioning

confidence: 99%

“…In macromolecular crystallography, the initial determination of phases by 'molecular replacement' (MR) (Rossmann & Blow, 1962;Huber, 1965;Rossmann, 1972;Lattman, 1985) is often attempted if the structure of a similar or homologous macromolecule is known ('search model'). MR involves the placement (i.e.…”

Section: Introductionmentioning

confidence: 99%

Extension of molecular replacement: a new search strategy based on Patterson correlation refinement

Brünger¹

1990

Acta Cryst Sect A

313

118

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“…Each search model was placed in a large P1 ce!l; Patterson vectors of 30-45 A., a resolution range of 10-4 A and a map grid size of 0.3 _A were chosen. Lattman angle grids 01 +03, 02 and 01-03 were searched with step sizes of A/cos(02/2), .4 and .4/sin(02/2 ) respectively, where .4=0.25 ° (Lattman, 1985). The 6000 highest peaks of the rotation function were collected into clusters of width 10 °, reduced to about 200 peaks and ordered by maximum height.…”

Section: Data Collectionmentioning

confidence: 99%

Structure of apo duck ovotransferrin: the structures of the N and C lobes are in the open form

Rawas

Muirhead²,

Williams³

1997

Acta Cryst D

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The structure of apo duck ovotransfemn (APODOT) has been determined at a resolution of 4.0A by the molecular replacement method using the structure of duck ovotransfemn (DOT) as the search model. The DOT structure contains two iron binding sites; one in the N-terminal lobe lying between domains N1 and N2 and one in the C-terminal lobe between domains C 1 and C2. Both lobes have a closed structure. Models of various forms of both the N and C lobes were used in the search. The final model was refined to give an R factor of 0.22. The comparison of the structure of APODOT with that of DOT shows that both the N and the C lobes are in an open form, where the N2 and C2 domains undergo large rigid-body rotations of 51.6 and 49.9 ° relative to the N1 and C1 domains, respectively. The interface between the N and C lobes, which is formed by the N1--C 1 contact in the core of the molecule does not change significantly. The DOT molecule may be described in terms of three rigid bodies; the N1 and C1 domains as one rigid body forming the static core of the molecule and the N2 and C2 domains as two other rigid bodies which, on the release of iron, move away from the static core of the molecule to form the open structure of APODOT.

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“…It is convenient to generate these assuming that the model lies at the origin of a P1 cell with`crystal' axes at least twice the model diameter. Many packages such as AMoRe use model structure factors which are more ®nely sampled in reciprocal space; i.e the`crystal' into which the model is placed has axes three or four times the model diameter (Lattman, 1985;Navaza, 2001). This means that the structure factors corresponding to different orientations of the model can be obtained by interpolation from the initial set.…”

Section: Introductionmentioning

confidence: 99%