Difference between revisions of "User Stories:BETA-BLIP"

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The case of β-lactamase (BETA)–β-
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{|class="wikitable" width=100%
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lactamase inhibitor (BLIP) has been
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|+ Crystallographic details
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used repeatedly as a test case for Phaser
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! Parameter !! Value !! Comment
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(Storoni et al., 2004; McCoy et al., 2005)
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|-
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because the original structure solution
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!Space Group
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by MR using AMoRe (Navaza, 1994)
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| P3₂21 || enantiomorphic with P3₁21
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was difficult even though good models
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|-
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were available (the structures of both
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!Unit Cell
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components had already been solved in
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| 75Å 75Å 133Å 90° 90° 120° || average
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isolation; Strynadka et al., 1996; Fig. 4a).
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|-
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The difficult part of the MR solution
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!Resolution
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was placing BLIP.
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| 2.5Å || average
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The command script for the solution
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|-
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of BETA–BLIP using the ‘automated
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!Solvent Content
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MR’ mode of Phaser is shown in
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| ~50% || average
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Appendix A1. The search order is given as BETA and then
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|-
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BLIP. This is because BETA, with 62% of the molecular
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!ASU Contents
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weight, would be expected to have the highest fraction scattering
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| 1×BETA + 1×BLIP || protein-protein complex
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(and indeed it does, as the B factors for BETA and
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|-
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BLIP are comparable). Phaser rapidly produces a correct
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!Model Quality
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solution for the complex. This previously difficult structure
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| 100%  identity || Both solved independently
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solution becomes trivial because of two algorithms implemented
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|-
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in Phaser. The first is the anisotropy correction; there
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!Anomalous atoms
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is significant anisotropy in the data (the maximum B-factor
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| N/A ||
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difference in different directions is 32 A ° 2). The second is the
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|-
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improved rotation-function target in MLRF, particularly in
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!Wavelength
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that the solution for BETA can be used to find the correct
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| N/A ||
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rotation-function solution for BLIP. Using the traditional
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|}
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Crowther (1972) fast rotation function, the Z score for the
 
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correct BLIP placement is 3.8 and the top Z score of 4.4
 
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corresponds to an incorrect placement. Using MLRF and the
 
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prior knowledge about the placement of BETA, the correct
 
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placement of BLIP has a Z score of 6.5 and is the highest score
 
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in the search. (These results are for data that have had the
 
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anisotropy correction applied, to illustrate the improvement
 
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given by the MLRF alone.)
 
  
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This example is illustrative of the case where one component
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;Story
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of the asymmetric unit is easy to find in isolation and
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The case of β-lactamase (BETA)–β-lactamase inhibitor (BLIP) has been used repeatedly as a test case for Phaser because the original structure solution by MR using AMoRe was difficult even though good models were available (the structures of both components had already been solved in isolation). The difficult part of the MR solution was placing BLIP. Phaser rapidly produces a correct solution for the complex.
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another is difficult or impossible to find. Knowledge of the
+
 
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partial structure of the component that is easy to find, introduced
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This previously difficult structure solution becomes trivial because of two algorithms implemented in Phaser.
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using the maximum-likelihood algorithms, enables the
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complex to be easily built up by addition.
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*The anisotropy correction; there is significant anisotropy in the data (the maximum B-factor difference in different directions is 32 Ų).
 +
*The improved rotation-function target in MLRF, particularly in that the solution for BETA can be used to find the correct rotation-function solution for BLIP. Using the traditional Crowther (1972) fast rotation function, the Z score for the correct BLIP placement is 3.8 and the top Z score of 4.4 corresponds to an incorrect placement. Using MLRF and the prior knowledge about the placement of BETA, the correct placement of BLIP has a Z score of 6.5 and is the highest score in the search. (These results are for data that have had the anisotropy correction applied, to illustrate the improvement given by the MLRF alone.)
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;Keyword script(s)
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<pre>
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MODE MR_AUTO
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HKLIN beta_blip.mtz
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LABIN F=Fobs SIGF=Sigma
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ENSEMBLE BETA PDB beta.pdb ID 100
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ENSEMBLE BLIP PDB blip.pdb ID 100
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SEARCH ENSEMBLE BETA
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SEARCH ENSEMBLE BLIP
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</pre>
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;Reference(s)
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:[http://antarctic/phaserwiki/images/4/40/Ba5095.pdf Solving structures of protein complexes by molecular replacement with Phaser ]
 +
:McCoy AJ
 +
:Acta Cryst. (2007). D63, 32-41

Latest revision as of 14:16, 24 February 2014

Crystallographic details
Parameter Value Comment
Space Group P3₂21 enantiomorphic with P3₁21
Unit Cell 75Å 75Å 133Å 90° 90° 120° average
Resolution 2.5Å average
Solvent Content ~50% average
ASU Contents 1×BETA + 1×BLIP protein-protein complex
Model Quality 100% identity Both solved independently
Anomalous atoms N/A
Wavelength N/A
Story

The case of β-lactamase (BETA)–β-lactamase inhibitor (BLIP) has been used repeatedly as a test case for Phaser because the original structure solution by MR using AMoRe was difficult even though good models were available (the structures of both components had already been solved in isolation). The difficult part of the MR solution was placing BLIP. Phaser rapidly produces a correct solution for the complex.

This previously difficult structure solution becomes trivial because of two algorithms implemented in Phaser.

  • The anisotropy correction; there is significant anisotropy in the data (the maximum B-factor difference in different directions is 32 Ų).
  • The improved rotation-function target in MLRF, particularly in that the solution for BETA can be used to find the correct rotation-function solution for BLIP. Using the traditional Crowther (1972) fast rotation function, the Z score for the correct BLIP placement is 3.8 and the top Z score of 4.4 corresponds to an incorrect placement. Using MLRF and the prior knowledge about the placement of BETA, the correct placement of BLIP has a Z score of 6.5 and is the highest score in the search. (These results are for data that have had the anisotropy correction applied, to illustrate the improvement given by the MLRF alone.)


Keyword script(s)
MODE MR_AUTO
HKLIN beta_blip.mtz
LABIN F=Fobs SIGF=Sigma
ENSEMBLE BETA PDB beta.pdb ID 100
ENSEMBLE BLIP PDB blip.pdb ID 100
SEARCH ENSEMBLE BETA
SEARCH ENSEMBLE BLIP
Reference(s)
Solving structures of protein complexes by molecular replacement with Phaser
McCoy AJ
Acta Cryst. (2007). D63, 32-41
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