2bn3: Difference between revisions

Line 1:

[[Image:2bn3.gif|left|200px]]<br /><applet load="2bn3" size="~~450~~" color="white" frame="true" align="right" spinBox="true"

[[Image:2bn3.gif|left|200px]]<br /><applet load="2bn3" size="350" color="white" frame="true" align="right" spinBox="true"

caption="2bn3, resolution 1.40Å" />

'''INSULIN BEFORE A HIGH DOSE X-RAY BURN'''<br />

==Overview==

Specific radiation damage can be used to solve macromolecular structures, using the radiation-damage-induced phasing (RIP) method. The method has, been investigated for six disulfide-containing test structures (elastase, insulin, lysozyme, ribonuclease A, trypsin and thaumatin) using data sets, that were collected on a third-generation synchrotron undulator beamline, with a highly attenuated beam. Each crystal was exposed to the, unattenuated X-ray beam between the collection of a 'before' and an, 'after' data set. The X-ray 'burn'-induced intensity differences ranged, from 5 to 15%, depending on the protein investigated. X-ray-susceptible, substructures were determined using the integrated direct and Patterson, methods in SHELXD. The best substructures were found by downscaling the, 'after' data set in SHELXC by a scale factor K, with optimal values, ranging from 0.96 to 0.99. The initial substructures were improved through, iteration with SHELXE by the addition of negatively occupied sites as well, as a large number of relatively weak sites. The final substructures ranged, from 40 to more than 300 sites, with strongest peaks as high as 57sigma., All structures except one could be solved: it was not possible to find the, initial substructure for ribonuclease A, however, SHELXE iteration, starting with the known five most susceptible sites gave excellent maps., Downscaling proved to be necessary for the solution of elastase, lysozyme, and thaumatin and reduced the number of SHELXE iterations in the other, cases. The combination of downscaling and substructure iteration provides, important benefits for the phasing of macromolecular structures using, radiation damage.

Specific radiation damage can be used to solve macromolecular structures using the radiation-damage-induced phasing (RIP) method. The method has been investigated for six disulfide-containing test structures (elastase, insulin, lysozyme, ribonuclease A, trypsin and thaumatin) using data sets that were collected on a third-generation synchrotron undulator beamline with a highly attenuated beam. Each crystal was exposed to the unattenuated X-ray beam between the collection of a 'before' and an 'after' data set. The X-ray 'burn'-induced intensity differences ranged from 5 to 15%, depending on the protein investigated. X-ray-susceptible substructures were determined using the integrated direct and Patterson methods in SHELXD. The best substructures were found by downscaling the 'after' data set in SHELXC by a scale factor K, with optimal values ranging from 0.96 to 0.99. The initial substructures were improved through iteration with SHELXE by the addition of negatively occupied sites as well as a large number of relatively weak sites. The final substructures ranged from 40 to more than 300 sites, with strongest peaks as high as 57sigma. All structures except one could be solved: it was not possible to find the initial substructure for ribonuclease A, however, SHELXE iteration starting with the known five most susceptible sites gave excellent maps. Downscaling proved to be necessary for the solution of elastase, lysozyme and thaumatin and reduced the number of SHELXE iterations in the other cases. The combination of downscaling and substructure iteration provides important benefits for the phasing of macromolecular structures using radiation damage.

==About this Structure==

2BN3 is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://~~ispc~~.weizmann.ac.il/oca-bin/ocashort?id=2BN3 OCA].

2BN3 is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2BN3 OCA].

==Reference==

Line 13:

[[Category: Bos taurus]]

[[Category: Protein complex]]

[[Category: Nanao, M.H.]]

[[Category: Nanao, M H.]]

[[Category: Ravelli, R.B.]]

[[Category: Ravelli, R B.]]

[[Category: carbohydrate metabolism]]

[[Category: direct protein sequencing]]

Line 26:

[[Category: synchrotron]]

''Page seeded by [http://~~ispc~~.weizmann.ac.il/oca OCA ] on ~~Wed Nov~~ 21 08:50:~~20 2007~~''

''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 16:39:37 2008''

Navigation menu

Page actions

Page actions

Personal tools

Navigation

Search

Tools

@@ Line 1: / Line 1: @@
-[[Image:2bn3.gif|left|200px]]<br /><applet load="2bn3" size="450" color="white" frame="true" align="right" spinBox="true"
+[[Image:2bn3.gif|left|200px]]<br /><applet load="2bn3" size="350" color="white" frame="true" align="right" spinBox="true"
 caption="2bn3, resolution 1.40&Aring;" />
 '''INSULIN BEFORE A HIGH DOSE X-RAY BURN'''<br />
 ==Overview==
-Specific radiation damage can be used to solve macromolecular structures, using the radiation-damage-induced phasing (RIP) method. The method has, been investigated for six disulfide-containing test structures (elastase, insulin, lysozyme, ribonuclease A, trypsin and thaumatin) using data sets, that were collected on a third-generation synchrotron undulator beamline, with a highly attenuated beam. Each crystal was exposed to the, unattenuated X-ray beam between the collection of a 'before' and an, 'after' data set. The X-ray 'burn'-induced intensity differences ranged, from 5 to 15%, depending on the protein investigated. X-ray-susceptible, substructures were determined using the integrated direct and Patterson, methods in SHELXD. The best substructures were found by downscaling the, 'after' data set in SHELXC by a scale factor K, with optimal values, ranging from 0.96 to 0.99. The initial substructures were improved through, iteration with SHELXE by the addition of negatively occupied sites as well, as a large number of relatively weak sites. The final substructures ranged, from 40 to more than 300 sites, with strongest peaks as high as 57sigma., All structures except one could be solved: it was not possible to find the, initial substructure for ribonuclease A, however, SHELXE iteration, starting with the known five most susceptible sites gave excellent maps., Downscaling proved to be necessary for the solution of elastase, lysozyme, and thaumatin and reduced the number of SHELXE iterations in the other, cases. The combination of downscaling and substructure iteration provides, important benefits for the phasing of macromolecular structures using, radiation damage.
+Specific radiation damage can be used to solve macromolecular structures using the radiation-damage-induced phasing (RIP) method. The method has been investigated for six disulfide-containing test structures (elastase, insulin, lysozyme, ribonuclease A, trypsin and thaumatin) using data sets that were collected on a third-generation synchrotron undulator beamline with a highly attenuated beam. Each crystal was exposed to the unattenuated X-ray beam between the collection of a 'before' and an 'after' data set. The X-ray 'burn'-induced intensity differences ranged from 5 to 15%, depending on the protein investigated. X-ray-susceptible substructures were determined using the integrated direct and Patterson methods in SHELXD. The best substructures were found by downscaling the 'after' data set in SHELXC by a scale factor K, with optimal values ranging from 0.96 to 0.99. The initial substructures were improved through iteration with SHELXE by the addition of negatively occupied sites as well as a large number of relatively weak sites. The final substructures ranged from 40 to more than 300 sites, with strongest peaks as high as 57sigma. All structures except one could be solved: it was not possible to find the initial substructure for ribonuclease A, however, SHELXE iteration starting with the known five most susceptible sites gave excellent maps. Downscaling proved to be necessary for the solution of elastase, lysozyme and thaumatin and reduced the number of SHELXE iterations in the other cases. The combination of downscaling and substructure iteration provides important benefits for the phasing of macromolecular structures using radiation damage.
 ==About this Structure==
-BN3 is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=2BN3 OCA].
+BN3 is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2BN3 OCA].
 ==Reference==
@@ Line 13: / Line 13: @@
 [[Category: Bos taurus]]
 [[Category: Protein complex]]
-[[Category: Nanao, M.H.]]
+[[Category: Nanao, M H.]]
-[[Category: Ravelli, R.B.]]
+[[Category: Ravelli, R B.]]
 [[Category: carbohydrate metabolism]]
 [[Category: direct protein sequencing]]
@@ Line 26: / Line 26: @@
 [[Category: synchrotron]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 08:50:20 2007''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 16:39:37 2008''