Difference between revisions of "User Stories:BETA-BLIP"
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| − | The case of β-lactamase (BETA)–β- | + | 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 (Navaza, 1994) was difficult even though good models were available (the structures of both components had already been solved in isolation; Strynadka et al., 1996). The difficult part of the MR solution was placing BLIP. The command script for the solution of BETA–BLIP using the ‘automated MR’ mode of Phaser is shown in Appendix A1. The search order is given as BETA and then BLIP. This is because BETA, with 62% of the molecular weight, would be expected to have the highest fraction scattering (and indeed it does, as the B factors for BETA and BLIP are comparable). Phaser rapidly produces a correct solution for the complex. |
| − | lactamase inhibitor (BLIP) has been | + | |
| − | used repeatedly as a test case for Phaser | + | This previously difficult structure solution becomes trivial because of two algorithms implemented in Phaser. *The first is the anisotropy correction; there is significant anisotropy in the data (the maximum B-factor difference in different directions is 32 Ų). |
| − | + | *The second is 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.) | |
| − | because the original structure solution | ||
| − | by MR using AMoRe (Navaza, 1994) | ||
| − | was difficult even though good models | ||
| − | were available (the structures of both | ||
| − | components had already been solved in | ||
| − | isolation; Strynadka et al., 1996 | ||
| − | The difficult part of the MR solution | ||
| − | was placing BLIP. | ||
| − | The command script for the solution | ||
| − | of BETA–BLIP using the ‘automated | ||
| − | MR’ mode of Phaser is shown in | ||
| − | Appendix A1. The search order is given as BETA and then | ||
| − | BLIP. This is because BETA, with 62% of the molecular | ||
| − | weight, would be expected to have the highest fraction scattering | ||
| − | (and indeed it does, as the B factors for BETA and | ||
| − | BLIP are comparable). Phaser rapidly produces a correct | ||
| − | solution for the complex. This previously difficult structure | ||
| − | solution becomes trivial because of two algorithms implemented | ||
| − | in Phaser. The first is the anisotropy correction; there | ||
| − | is significant anisotropy in the data (the maximum B-factor | ||
| − | difference in different directions is 32 | ||
| − | 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.) | ||
Revision as of 21:20, 11 July 2009
| Space Group | P3221 |
|---|---|
| Unit Cell | |
| Contents of asymmetric unit |
BETA and BLIP |
| Models | 100% identity |
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 (Navaza, 1994) was difficult even though good models were available (the structures of both components had already been solved in isolation; Strynadka et al., 1996). The difficult part of the MR solution was placing BLIP. The command script for the solution of BETA–BLIP using the ‘automated MR’ mode of Phaser is shown in Appendix A1. The search order is given as BETA and then BLIP. This is because BETA, with 62% of the molecular weight, would be expected to have the highest fraction scattering (and indeed it does, as the B factors for BETA and BLIP are comparable). Phaser rapidly produces a correct solution for the complex.
This previously difficult structure solution becomes trivial because of two algorithms implemented in Phaser. *The first is the anisotropy correction; there is significant anisotropy in the data (the maximum B-factor difference in different directions is 32 Ų).
- The second is 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.)
