User Stories:BETA-BLIP - Revision history

Airlie at 13:16, 24 February 2014

2014-02-24T13:16:24Z

WikiSysop: add image

2009-07-16T14:13:18Z

add image

WikiSysop: unit cell Å and °

2009-07-11T21:39:25Z

unit cell Å and °

WikiSysop: edit table to fit template

2009-07-11T21:38:21Z

edit table to fit template

WikiSysop: crystallographic table

2009-07-11T21:19:39Z

crystallographic table

WikiSysop: edit, add script and reference

2009-07-11T20:31:06Z

edit, add script and reference

WikiSysop at 20:21, 11 July 2009

2009-07-11T20:21:06Z

WikiSysop: formatting

2009-07-11T20:20:45Z

formatting

WikiSysop: add crystallographic table

2009-07-11T16:31:18Z

add crystallographic table

WikiSysop: delete last paragraph about "this example is illustrative..."

2009-07-09T11:57:44Z

delete last paragraph about "this example is illustrative..."

← Older revision		Revision as of 13:16, 24 February 2014
Line 52:		Line 52:
	:McCoy AJ		:McCoy AJ
	:Acta Cryst. (2007). D63, 32-41		:Acta Cryst. (2007). D63, 32-41
−
−	~~;Figures~~
−	~~[[Image:beta_blip.gif\|left\|frame\|Structure of the β-lactamase (BETA)–β-lactamase inhibitor (BLIP) complex. BETA is in blue and BLIP is in yellow]]~~

← Older revision		Revision as of 14:13, 16 July 2009
Line 52:		Line 52:
	:McCoy AJ		:McCoy AJ
	:Acta Cryst. (2007). D63, 32-41		:Acta Cryst. (2007). D63, 32-41
		+
		+	;Figures
		+	[[Image:beta_blip.gif\|left\|frame\|Structure of the β-lactamase (BETA)–β-lactamase inhibitor (BLIP) complex. BETA is in blue and BLIP is in yellow]]

@@ Line 7: / Line 7: @@
 |-
 !Unit Cell
-| 75 75 133 90 90 120 || average
+| 75Å 75Å 133Å 90° 90° 120° || average
 |-
 !Resolution

@@ Line 1: / Line 1: @@
-{|class="wikitable" align=right style="margin-left: 30px"
+{|class="wikitable" width=100%
 |+ Crystallographic details
 ! Parameter !! Value !! Comment
@@ Line 12: / Line 12: @@
 | 2.5Å || average
 |-
-!Solvent
+!Solvent Content
 | ~50% || average
 |-
-!Contents of ASU
+!ASU Contents
 | 1×BETA + 1×BLIP || protein-protein complex
 |-
-!Model
+!Model Quality
 | 100%  identity || Both solved independently
 |-
 !Anomalous atoms
 | N/A ||
 |}
 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.
@@ Line 32: / Line 36: @@
 *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
 <pre>
 MODE MR_AUTO
@@ Line 43: / Line 48: @@
 </pre>
-;References
+;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

@@ Line 1: / Line 1: @@
-{|class="wikitable" align=right
+{|class="wikitable" align=right style="margin-left: 30px"
 |+ Crystallographic details
 |-
 !Space Group
-| P3221
+| P3₂21 || enantiomorphic with P3₁21
 |-
 !Unit Cell
+| 75 75 133 90 90 120 || average
 |-
-!Contents of<br>asymmetric unit
+!Resolution
-| BETA and BLIP
+| 2.5Å || average
 |-
-!Models
+!Solvent
-| 100% identity
+| ~50% || average
 |}

@@ Line 15: / Line 15: @@
 |}
-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.
+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 first is the anisotropy correction; there is significant anisotropy in the data (the maximum B-factor difference in different directions is 32 Å²).
+*The anisotropy correction; there is significant anisotropy in the data (the maximum B-factor difference in different directions is 32 Å²).
-*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.)
+*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.)

← Older revision		Revision as of 16:31, 11 July 2009
Line 1:		Line 1:
		+	{\|class="wikitable" align=right
		+	\|+ Crystallographic details
		+	\|-
		+	!Space Group
		+	\| P3221
		+	\|-
		+	!Unit Cell
		+	\|
		+	\|-
		+	!Contents of<br>asymmetric unit
		+	\| BETA and BLIP
		+	\|-
		+	!Models
		+	\| 100% identity
		+	\|}
		+
	The case of β-lactamase (BETA)–β-		The case of β-lactamase (BETA)–β-
	lactamase inhibitor (BLIP) has been		lactamase inhibitor (BLIP) has been

← Older revision		Revision as of 11:57, 9 July 2009
Line 35:		Line 35:
	anisotropy correction applied, to illustrate the improvement		anisotropy correction applied, to illustrate the improvement
	given by the MLRF alone.)		given by the MLRF alone.)
−
−	~~This example is illustrative of the case where one component~~
−	~~of the asymmetric unit is easy to find in isolation and~~
−	~~another is difficult or impossible to find. Knowledge of the~~
−	~~partial structure of the component that is easy to find, introduced~~
−	~~using the maximum-likelihood algorithms, enables the~~
−	~~complex to be easily built up by addition.~~