An approach to three-dimensional structures of biomolecules by using single-molecule diffraction images
- *Stanford Synchrotron Radiation Laboratory, Stanford Linear Accelerator Center, Stanford University, Stanford, CA 94309-0210; ‡Department of Chemistry, Stanford University, Stanford, CA 94305; and §Department of Physics and Astronomy, State University of New York, Stony Brook, NY 11794
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Edited by Douglas C. Rees, California Institute of Technology, Pasadena, CA, and approved April 2, 2001 (received for review February 20, 2001)
Abstract
We describe an approach to the high-resolution three-dimensional structural determination of macromolecules that utilizes ultrashort, intense x-ray pulses to record diffraction data in combination with direct phase retrieval by the oversampling technique. It is shown that a simulated molecular diffraction pattern at 2.5-Å resolution accumulated from multiple copies of single rubisco biomolecules, each generated by a femtosecond-level x-ray free electron laser pulse, can be successfully phased and transformed into an accurate electron density map comparable to that obtained by more conventional methods. The phase problem is solved by using an iterative algorithm with a random phase set as an initial input. The convergence speed of the algorithm is reasonably fast, typically around a few hundred iterations. This approach and phasing method do not require any ab initio information about the molecule, do not require an extended ordered lattice array, and can tolerate high noise and some missing intensity data at the center of the diffraction pattern. With the prospects of the x-ray free electron lasers, this approach could provide a major new opportunity for the high-resolution three-dimensional structure determination of single biomolecules.
Footnotes
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↵ † To whom reprint requests should be addressed. E-mail: miao{at}ssrl.slac.stanford.edu.
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This paper was submitted directly (Track II) to the PNAS office.
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See commentary on page 6535.
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↵ ‖ Given the diffraction pattern, one can calculate the Patterson function of the molecule. This function can provide an approximate envelope of the molecule, which could be a better finite support for the algorithm.
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↵ ¶ Another potential algorithm is the holographic reconstruction method. See, e.g., ref. 25.
- Abbreviations:
- 3D,
- three-dimensional;
- 2D,
- two-dimensional;
- X-FEL,
- x-ray free electron laser
- Copyright © 2001, The National Academy of Sciences
