Evaluating the solution from MrBUMP and BALBES - PubMed (original) (raw)

Evaluating the solution from MrBUMP and BALBES

Ronan M Keegan et al. Acta Crystallogr D Biol Crystallogr. 2011 Apr.

Abstract

Molecular replacement is one of the key methods used to solve the problem of determining the phases of structure factors in protein structure solution from X-ray image diffraction data. Its success rate has been steadily improving with the development of improved software methods and the increasing number of structures available in the PDB for use as search models. Despite this, in cases where there is low sequence identity between the target-structure sequence and that of its set of possible homologues it can be a difficult and time-consuming chore to isolate and prepare the best search model for molecular replacement. MrBUMP and BALBES are two recent developments from CCP4 that have been designed to automate and speed up the process of determining and preparing the best search models and putting them through molecular replacement. Their intention is to provide the user with a broad set of results using many search models and to highlight the best of these for further processing. An overview of both programs is presented along with a description of how best to use them, citing case studies and the results of large-scale testing of the software.

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Figures

Figure 1

Figure 1

The types and hierarchy of the search models presented in BALBES jobs.

Figure 2

Figure 2

A flow chart of the structural solution process in BALBES.

Figure 3

Figure 3

An example shows how BALBES combines models from different PDB files to obtain a complex solution.

Figure 4

Figure 4

(a) The top-level directory structure for a MrBUMP job. All job information is stored under a folder ‘search_JobID’, where JobID is the job identifier. The ‘data’ directory contains all of the processing data for each of the template search models. (b) The breakdown of the ‘data’ directory. There are potentially four model types created for each template search model. Each model-type directory contains the molecular-replacement and refinement files for that model.

Figure 5

Figure 5

This histogram shows a breakdown of where the top-scoring solution in each of the MrBUMP jobs ranked in terms of its initial ranking before being put through molecular replacement. This ranking is based on the score function for the search models. As can be seen, it often happens that the top-scoring solution lies outside the first five top-scoring search models.

Figure 6

Figure 6

A plot of the model types for the best-scoring search models after molecular replacement and refinement for each of the MrBUMP jobs in the test set. We only show results where a solution was deemed to be ‘marginal’ or better.

Figure 7

Figure 7

Example

2wfb

: crystal structure of the apo form of the orange protein (Apo-Orp) from Desulfovibrio gigas (S. Najmudin, C. Bonifacio, A. G. Duarte, I. Moura, J. G. Moura & M. G. Romao, unpublished work). This is an ensemble example where the constituent search models (

1rdu

_ A,

1eo1

_ A,

1o13

_ A,

1t3v

_ A) in the ensemble failed to yield an acceptable solution on their own using Phaser to perform the MR. The ensemble itself produced a ‘good’ solution. Providing Phaser with the ensemble of aligned search models allowed it to downweight the signal from parts of the models which are not conserved across all of the structures, i.e. flexible loops and terminal residues. The figure was prepared using CCP_4_mg (Potterton et al., 2004 ▶).

Figure 8

Figure 8

Example

2zzt

: crystal structure of the cytosolic domain of the cation-diffusion facilitator family protein. The smaller domain in

2qfi

(zinc transporter YiiP; green) matches the structure of

2zzt

(pink) very closely in its secondary-structure conformation. The figure was prepared using CCP_4_mg (Potterton et al., 2004 ▶).

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