23 Questions
Which factors are used as a first approximation for the unknown molecule in molecular replacement?
Structure factors and phases of a known structure
What do the amplitudes and phase angles depend on in molecular replacement?
Both the structure of the protein and its orientation within the unit cell
What is the main purpose of molecular replacement?
To approximate the structure of an unknown molecule using a known structure
The Patterson function is essentially the Fourier transform of the ______ rather than the structure factors
intensities
The Patterson map for the structure for which you are trying to compute phases is a ______ map
stationary
Which researcher introduced the Patterson function in X-ray crystallography?
Arthur Lindo Patterson
What does the Patterson map represent in X-ray crystallography?
The interatomic vectors
How many peaks does the Patterson space unit cell contain?
N^2
Which type of vectors cause peaks in a Patterson map?
Both intramolecular and intermolecular vectors
Where are intramolecular vectors located in a Patterson map?
Near origin
What are intermolecular vectors dependent on in a Patterson map?
Both position and orientation
Which scoring method is commonly used in modern programs for the rotation function?
Maximum likelihood-based algorithms
What is the key factor for obtaining high correlation scores in the rotation function?
Using different orientations
What is the purpose of the rotation function in X-ray crystallography?
To compare unknown Patterson maps
Which function is commonly used now instead of the brute-force search in the translation function?
Fast translation functions
What is the purpose of the translation function in X-ray crystallography?
To correctly position the known model
What is compared in the translation function to determine positions with high correlations?
The unknown-derived Patterson map
Which step is involved in the rotation function of molecular replacement?
Finding a homologous structure
Which resolution cutoff is typically used in the translation function of molecular replacement?
3.0 to 10.0Å
What determines the size of the integration radius in the rotation function of molecular replacement?
The size of the molecule
Which buffer is often used in protein purification?
Phosphate buffer
What are the heavy atom compounds that form insoluble aggregates with phosphate buffer?
Uranyl ions and rare earth elements
Which compound can be used as a replacement for Ammonium sulfate?
Li2SO4
Study Notes
The Patterson Function
- Introduced in 1935 by Arthur Lindo Patterson while working at MIT's laboratory of Bertram Eugene Warren.
- Solves the phase problem in X-ray crystallography.
- Essentially the Fourier transform of intensities rather than structure factors.
- Does not require phases.
The Patterson Map
- A representation of the interatomic vectors in the unit cell.
- Contains N2 peaks, corresponding to the N vectors that exist for each of the N atoms.
- Only a subset of Patterson vectors are chosen for comparison: the self Patterson peaks.
- The Patterson map for the structure being analyzed is a stationary map.
- The Patterson map for the search model is rotated.
Test your knowledge on Molecular Replacement with this quiz! Learn how this method uses the structure factors and phases of a similar structure to solve for the unknown molecule. Explore the role of protein structure and orientation in determining amplitudes and phase angles.
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