Podcast
Questions and Answers
Which factors are used as a first approximation for the unknown molecule in molecular replacement?
Which factors are used as a first approximation for the unknown molecule in molecular replacement?
- Amplitudes and phase angles of the unknown molecule
- Amplitudes and phase angles of a known structure
- Structure factors and phases of a known structure (correct)
- Structure factors and phases of the unknown molecule
What do the amplitudes and phase angles depend on in molecular replacement?
What do the amplitudes and phase angles depend on in molecular replacement?
- The orientation of the protein within the unit cell only
- Both the structure of the protein and its orientation within the unit cell (correct)
- Neither the structure nor the orientation of the protein
- The structure of the protein only
What is the main purpose of molecular replacement?
What is the main purpose of molecular replacement?
- To compare the amplitudes and phase angles of different molecules
- To calculate the structure factors and phases of an unknown molecule
- To approximate the structure of an unknown molecule using a known structure (correct)
- To determine the structure of a known molecule
The Patterson function is essentially the Fourier transform of the ______ rather than the structure factors
The Patterson function is essentially the Fourier transform of the ______ rather than the structure factors
The Patterson map for the structure for which you are trying to compute phases is a ______ map
The Patterson map for the structure for which you are trying to compute phases is a ______ map
Which researcher introduced the Patterson function in X-ray crystallography?
Which researcher introduced the Patterson function in X-ray crystallography?
What does the Patterson map represent in X-ray crystallography?
What does the Patterson map represent in X-ray crystallography?
How many peaks does the Patterson space unit cell contain?
How many peaks does the Patterson space unit cell contain?
Which type of vectors cause peaks in a Patterson map?
Which type of vectors cause peaks in a Patterson map?
Where are intramolecular vectors located in a Patterson map?
Where are intramolecular vectors located in a Patterson map?
What are intermolecular vectors dependent on in a Patterson map?
What are intermolecular vectors dependent on in a Patterson map?
Which scoring method is commonly used in modern programs for the rotation function?
Which scoring method is commonly used in modern programs for the rotation function?
What is the key factor for obtaining high correlation scores in the rotation function?
What is the key factor for obtaining high correlation scores in the rotation function?
What is the purpose of the rotation function in X-ray crystallography?
What is the purpose of the rotation function in X-ray crystallography?
Which function is commonly used now instead of the brute-force search in the translation function?
Which function is commonly used now instead of the brute-force search in the translation function?
What is the purpose of the translation function in X-ray crystallography?
What is the purpose of the translation function in X-ray crystallography?
What is compared in the translation function to determine positions with high correlations?
What is compared in the translation function to determine positions with high correlations?
Which step is involved in the rotation function of molecular replacement?
Which step is involved in the rotation function of molecular replacement?
Which resolution cutoff is typically used in the translation function of molecular replacement?
Which resolution cutoff is typically used in the translation function of molecular replacement?
What determines the size of the integration radius in the rotation function of molecular replacement?
What determines the size of the integration radius in the rotation function of molecular replacement?
Which buffer is often used in protein purification?
Which buffer is often used in protein purification?
What are the heavy atom compounds that form insoluble aggregates with phosphate buffer?
What are the heavy atom compounds that form insoluble aggregates with phosphate buffer?
Which compound can be used as a replacement for Ammonium sulfate?
Which compound can be used as a replacement for Ammonium sulfate?
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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.
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