Low Resolution ab initio Phasing Method by Modification of Density and Phase in Real and Reciprocal Space

Phasing problem in X-ray structure determination can be challenging. Several methods, such as Isomorphous Replacement and Molecule Replacement, are frequently used. But their success relies on the availability of either an isomorphous heavy-atom derivative or a high identity homologous model. In this thesis, a low resolution ab initio phasing method is proposed. A large number of trial phases value and their corresponding high density masks are generated and modified alternately in reciprocal and real space. Then, the output phase sets are averaged to give the estimated phases and figure of merit which are capable of capturing key feature of the molecules’ low resolution envelope by Fourier synthesis. Smoothed particle hydrodynamics is employed to animate the high density masks’ modification process. The method is tested and compared with Lunin’s connectivity-based phasing method which also takes advantage of geometric properties of high density masks.

Name thesis:degree_name

Master of Science

Level thesis:degree_level

Masters

Discipline thesis:degree_discipline

Natural Sciences

Grantor

Rice University

Year dc:date.issued

2013

Author dc:creator

• Liao, Yunxiang

Advisor dc:contributor.advisor

• Ma, Jianpeng

Committee members dc:contributor.committeemember

• Raphael, Robert M.
• Kiang, Ching-Hwa

• Ab initio phasing
• Low resolution

Statement dc:rights

• Copyright is held by the author, unless otherwise indicated. Permission to reuse, publish, or reproduce the work beyond the bounds of fair use or other exemptions to copyright law must be obtained from the copyright holder.

Language dc:language.iso

eng

Handle dc:identifier.uri

https://hdl.handle.net/1911/77194

OAI identifier oai:identifier

oai:repository.rice.edu:1911/77194