The direct rotation function: rotational Patterson correlation search applied to molecular replacement

1995 ◽  
Vol 51 (5) ◽  
pp. 740-748 ◽  
Author(s):  
W. L. DeLano ◽  
A. T. Brünger
Keyword(s):  
Molecular Replacement ◽  
Direct Rotation ◽  
Correlation Search ◽  
Rotation Function

scholarly journals Using a partial atomic model from medium-resolution cryo-EM to solve a large crystal structure

2021 ◽  
Vol 77 (1) ◽  
pp. 11-18
Author(s):  
Montserrat Fàbrega-Ferrer ◽  
Ana Cuervo ◽  
Francisco J. Fernández ◽  
Cristina Machón ◽  
Rosa Pérez-Luque ◽  
...  
Keyword(s):  
Molecular Replacement ◽  
Large Crystal ◽  
Rotation Matrices ◽  
Cryo Electron Microscopy ◽  
Partial Models ◽  
Medium Resolution ◽  
Experimental Phasing ◽  
Crystallographic Structures ◽  
Direct Use ◽  
Rotation Function

Medium-resolution cryo-electron microscopy maps, in particular when they include a significant number of α-helices, may allow the building of partial models that are useful for molecular-replacement searches in large crystallographic structures when the structures of homologs are not available and experimental phasing has failed. Here, as an example, the solution of the structure of a bacteriophage portal using a partial 30% model built into a 7.8 Å resolution cryo-EM map is shown. Inspection of the self-rotation function allowed the correct oligomerization state to be determined, and density-modification procedures using rotation matrices and a mask based on the cryo-EM structure were critical for solving the structure. A workflow is described that may be applicable to similar cases and this strategy is compared with direct use of the cryo-EM map for molecular replacement.

scholarly journals Using Phaser and ensembles to improve the performance of SIMBAD

2020 ◽  
Vol 76 (1) ◽  
pp. 1-8 ◽  
Author(s):  
Adam J. Simpkin ◽  
Felix Simkovic ◽  
Jens M. H. Thomas ◽  
Martin Savko ◽  
Andrey Lebedev ◽  
...  
Keyword(s):  
Model Identification ◽  
Structural Similarity ◽  
Test Cases ◽  
Target Sequence ◽  
Molecular Replacement ◽  
Search Models ◽  
Termination Criteria ◽  
Alternative Approach ◽  
The Relationship ◽  
Rotation Function

The conventional approach to search-model identification in molecular replacement (MR) is to screen a database of known structures using the target sequence. However, this strategy is not always effective, for example when the relationship between sequence and structural similarity fails or when the crystal contents are not those expected. An alternative approach is to identify suitable search models directly from the experimental data. SIMBAD is a sequence-independent MR pipeline that uses either a crystal lattice search or MR functions to directly locate suitable search models from databases. The previous version of SIMBAD used the fast AMoRe rotation-function search. Here, a new version of SIMBAD which makes use of Phaser and its likelihood scoring to improve the sensitivity of the pipeline is presented. It is shown that the additional compute time potentially required by the more sophisticated scoring is counterbalanced by the greater sensitivity, allowing more cases to trigger early-termination criteria, rather than running to completion. Using Phaser solved 17 out of 25 test cases in comparison to the ten solved with AMoRe, and it is shown that use of ensemble search models produces additional performance benefits.

AUTOMR: an automatic processing program system for the molecular replacement method

1991 ◽  
Vol 24 (6) ◽  
pp. 1063-1066 ◽  
Author(s):  
Y. Matsuura
Keyword(s):  
Automatic Processing ◽  
Molecular Replacement ◽  
Initial Model ◽  
Program System ◽  
Replacement Method ◽  
Model Molecule ◽  
Translation Function ◽  
Processing Program ◽  
Molecular Replacement Method ◽  
Rotation Function

An automatic processing program system of the molecular replacement method AUTOMR is presented. The program solves the initial model of the target crystal structure using a homologous molecule as the search model. It processes the structure-factor calculation of the model molecule, the rotation function, the translation function and the rigid-group refinement successively in one computer job. Test calculations were performed for six protein crystals and the structures were solved in all of these cases.

OVIONE: a new vector-search rotation-function program for macromolecular crystallography

2000 ◽  
Vol 33 (6) ◽  
pp. 1436-1444
Author(s):  
Carmen Álvarez-Rúa ◽  
Javier Borge ◽  
Santiago García-Granda
Keyword(s):  
Crystal Structure ◽  
Careful Analysis ◽  
Molecular Replacement ◽  
Macromolecular Crystallography ◽  
Minimization Algorithm ◽  
Statistical Parameters ◽  
Replacement Method ◽  
Molecular Replacement Method ◽  
Rotation Function ◽  
Selection Of

A computer program (OVIONE) that uses a new vector-search rotation function for crystal-structure determination by the molecular-replacement method has been developed. Image-seeking functions have proved to be useful rotation functions in macromolecular crystallography, provided that some conditions on the statistical parameters of both the crystal and the model Patterson maps are fulfilled. An appropriate selection of the vectors involved in the calculation of the image-seeking functions is crucial for the success of the proposed procedure. This selection relies on certain parameters, a careful analysis of which has been performed in order to establish optimal ranges in which the discrimination of the rotation function is enhanced. Finally, the refinement of the highest peaks of the rotation function is carried out by making use of a simple and quick minimization algorithm.

Electron microscopy of rabbit FC crystals

1983 ◽  
Vol 41 ◽  
pp. 730-731
Author(s):  
Robert A. Grant ◽  
Laura L. Degn ◽  
Wah Chiu ◽  
John Robinson
Keyword(s):  
Electron Microscopy ◽  
High Resolution ◽  
High Resolution Electron Microscopy ◽  
Molecular Replacement ◽  
X Ray ◽  
X Ray Crystallography ◽  
Resolution Electron ◽  
Replacement Technique ◽  
Hydrated Crystal ◽  
Molecular Structure Analysis

Proteolytic digestion of the immunoglobulin IgG with papain cleaves the molecule into an antigen binding fragment, Fab, and a compliment binding fragment, Fc. Structures of intact immunoglobulin, Fab and Fc from various sources have been solved by X-ray crystallography. Rabbit Fc can be crystallized as thin platelets suitable for high resolution electron microscopy. The structure of rabbit Fc can be expected to be similar to the known structure of human Fc, making it an ideal specimen for comparing the X-ray and electron crystallographic techniques and for the application of the molecular replacement technique to electron crystallography. Thin protein crystals embedded in ice diffract to high resolution. A low resolution image of a frozen, hydrated crystal can be expected to have a better contrast than a glucose embedded crystal due to the larger density difference between protein and ice compared to protein and glucose. For these reasons we are using an ice embedding technique to prepare the rabbit Fc crystals for molecular structure analysis by electron microscopy.

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