Difference between revisions of "User Stories:BETA-BLIP"
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| − | {|class="wikitable" | + | {|class="wikitable" width=100% |
|+ Crystallographic details | |+ Crystallographic details | ||
| + | ! Parameter !! Value !! Comment | ||
|- | |- | ||
!Space Group | !Space Group | ||
| − | | | + | | P3₂21 || enantiomorphic with P3₁21 |
|- | |- | ||
!Unit Cell | !Unit Cell | ||
| − | | | + | | 75Å 75Å 133Å 90° 90° 120° || average |
|- | |- | ||
| − | ! | + | !Resolution |
| − | | | + | | 2.5Å || average |
|- | |- | ||
| − | ! | + | !Solvent Content |
| − | | 100% identity | + | | ~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. | 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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*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.) | *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 | + | |
| + | ;Keyword script(s) | ||
<pre> | <pre> | ||
MODE MR_AUTO | MODE MR_AUTO | ||
| Line 33: | Line 48: | ||
</pre> | </pre> | ||
| − | ; | + | ;Reference(s) |
:[http://antarctic/phaserwiki/images/4/40/Ba5095.pdf Solving structures of protein complexes by molecular replacement with Phaser ] | :[http://antarctic/phaserwiki/images/4/40/Ba5095.pdf Solving structures of protein complexes by molecular replacement with Phaser ] | ||
:McCoy AJ | :McCoy AJ | ||
:Acta Cryst. (2007). D63, 32-41 | :Acta Cryst. (2007). D63, 32-41 | ||
Latest revision as of 14:16, 24 February 2014
| 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
