This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.
Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.




2bly

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Line 1: Line 1:
-
[[Image:2bly.gif|left|200px]]
+
{{Seed}}
 +
[[Image:2bly.png|left|200px]]
<!--
<!--
Line 9: Line 10:
{{STRUCTURE_2bly| PDB=2bly | SCENE= }}
{{STRUCTURE_2bly| PDB=2bly | SCENE= }}
-
'''HEWL AFTER A HIGH DOSE X-RAY "BURN"'''
+
===HEWL AFTER A HIGH DOSE X-RAY "BURN"===
-
==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.
+
The line below this paragraph, {{ABSTRACT_PUBMED_16131756}}, adds the Publication Abstract to the page
 +
(as it appears on PubMed at http://www.pubmed.gov), where 16131756 is the PubMed ID number.
 +
-->
 +
{{ABSTRACT_PUBMED_16131756}}
==About this Structure==
==About this Structure==
Line 33: Line 37:
[[Category: Rip]]
[[Category: Rip]]
[[Category: Synchrotron]]
[[Category: Synchrotron]]
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May 3 20:28:22 2008''
+
 
 +
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Jul 27 22:51:56 2008''

Revision as of 19:51, 27 July 2008

Image:2bly.png

Template:STRUCTURE 2bly

HEWL AFTER A HIGH DOSE X-RAY "BURN"

Template:ABSTRACT PUBMED 16131756

About this Structure

2BLY is a Single protein structure of sequence from Gallus gallus. Full crystallographic information is available from OCA.

Reference

Improving radiation-damage substructures for RIP., Nanao MH, Sheldrick GM, Ravelli RB, Acta Crystallogr D Biol Crystallogr. 2005 Sep;61(Pt 9):1227-37. Epub 2005, Aug 16. PMID:16131756

Page seeded by OCA on Sun Jul 27 22:51:56 2008

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2bly"
Personal tools