Difference between revisions of "User Stories:BETA-BLIP"
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− | The case of β-lactamase (BETA)–β- | + | {|class="wikitable" width=100% |
− | lactamase inhibitor (BLIP) has been | + | |+ Crystallographic details |
− | used repeatedly as a test case for Phaser | + | ! Parameter !! Value !! Comment |
− | + | |- | |
− | because the original structure solution | + | !Space Group |
− | by MR using AMoRe | + | | P3₂21 || enantiomorphic with P3₁21 |
− | was difficult even though good models | + | |- |
− | were available (the structures of both | + | !Unit Cell |
− | components had already been solved in | + | | 75Å 75Å 133Å 90° 90° 120° || average |
− | isolation | + | |- |
− | The difficult part of the MR solution | + | !Resolution |
− | was placing BLIP | + | | 2.5Å || average |
− | + | |- | |
− | + | !Solvent Content | |
− | + | | ~50% || average | |
− | + | |- | |
− | + | !ASU Contents | |
− | + | | 1×BETA + 1×BLIP || protein-protein complex | |
− | + | |- | |
− | + | !Model Quality | |
− | solution for the complex. This previously difficult structure | + | | 100% identity || Both solved independently |
− | solution becomes trivial because of two algorithms implemented | + | |- |
− | in Phaser. The | + | !Anomalous atoms |
− | is significant anisotropy in the data (the maximum B-factor | + | | N/A || |
− | difference in different directions is 32 | + | |- |
− | improved rotation-function target in MLRF, particularly in | + | !Wavelength |
− | that the solution for BETA can be used to find the correct | + | | N/A || |
− | 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 | + | ;Story |
− | corresponds to an incorrect placement. Using MLRF and the | + | 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. |
− | prior knowledge about the placement of BETA, the correct | + | |
− | placement of BLIP has a Z score of 6.5 and is the highest score | + | This previously difficult structure solution becomes trivial because of two algorithms implemented in Phaser. |
− | in the search. (These results are for data that have had the | + | |
− | anisotropy correction applied, to illustrate the improvement | + | *The anisotropy correction; there is significant anisotropy in the data (the maximum B-factor difference in different directions is 32 Ų). |
− | 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(s) | ||
+ | <pre> | ||
+ | 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 | ||
+ | </pre> | ||
+ | |||
+ | ;Reference(s) | ||
+ | :[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
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