Podcast
Questions and Answers
Which method is used to calculate the electron density map?
Which method is used to calculate the electron density map?
- Diffraction intensity
- Unknown phasing model
- Observed structure factor amplitude (correct)
- Molecular replacement solution
Which component provides more structural information in the calculation of the electron density map?
Which component provides more structural information in the calculation of the electron density map?
- Observed structure factor amplitude
- Theoretical phases (correct)
- Molecular replacement solution
- Diffraction intensity
Which statement is true about the bias in the calculated structure?
Which statement is true about the bias in the calculated structure?
- The calculated structure is never biased towards the phasing model
- The bias in the calculated structure is independent of the phasing model
- The calculated structure is always biased towards the phasing model
- The bias in the calculated structure depends on the similarity between the phasing model and the unknown (correct)
Which method can be used to treat the model bias problem in molecular replacement?
Which method can be used to treat the model bias problem in molecular replacement?
What is the expected outcome of using a poly-alanine model for molecular replacement?
What is the expected outcome of using a poly-alanine model for molecular replacement?
What should the resulting map from a composite omit map calculation contain?
What should the resulting map from a composite omit map calculation contain?
Which unit cell has a 5-fold NCS in this example?
Which unit cell has a 5-fold NCS in this example?
What needs to be defined in order to apply NCS averaging?
What needs to be defined in order to apply NCS averaging?
Which parameter describes the degree of order of an atom?
Which parameter describes the degree of order of an atom?
What is the range of values for the occupancy parameter?
What is the range of values for the occupancy parameter?
How many parameters are assigned to every atom in the PDB file generated by model building?
How many parameters are assigned to every atom in the PDB file generated by model building?
Atomic models contain a large number of ______
Atomic models contain a large number of ______
Inclusion of stereochemical data significantly increase the number of ______
Inclusion of stereochemical data significantly increase the number of ______
_______ can be applied in two different ways
_______ can be applied in two different ways
Which file format describes the three-dimensional structures of molecules in the Protein Data Bank?
Which file format describes the three-dimensional structures of molecules in the Protein Data Bank?
What is the ratio of observations to parameters in the refinement process of the papain crystal structure?
What is the ratio of observations to parameters in the refinement process of the papain crystal structure?
What type of data significantly increases the number of observations in the refinement process?
What type of data significantly increases the number of observations in the refinement process?
How are stereochemical data applied in the refinement process?
How are stereochemical data applied in the refinement process?
What parameters are assigned to every atom in the PDB file generated by model building?
What parameters are assigned to every atom in the PDB file generated by model building?
Which degrees of freedom are minimized for each group of atoms specified as a rigid body?
Which degrees of freedom are minimized for each group of atoms specified as a rigid body?
What is the purpose of rigid body refinement in the early stages of refinement?
What is the purpose of rigid body refinement in the early stages of refinement?
How can the entire model be treated in rigid body refinement?
How can the entire model be treated in rigid body refinement?
Which technique is commonly used for finding the best fit of the model to the data in protein crystallography?
Which technique is commonly used for finding the best fit of the model to the data in protein crystallography?
What is the purpose of position refinement in protein crystallography?
What is the purpose of position refinement in protein crystallography?
Which parameter is fixed to ideal values in torsional refinement?
Which parameter is fixed to ideal values in torsional refinement?
What does torsional refinement reduce in the refinement process?
What does torsional refinement reduce in the refinement process?
In torsional refinement, atoms are grouped into what?
In torsional refinement, atoms are grouped into what?
Which factor is indicated by high B-values in protein crystallography?
Which factor is indicated by high B-values in protein crystallography?
What does the B-factor relate to in protein crystallography?
What does the B-factor relate to in protein crystallography?
What does a high B-factor value suggest in protein crystallography?
What does a high B-factor value suggest in protein crystallography?
Which factor is used to describe disorder in the model?
Which factor is used to describe disorder in the model?
What is the upper limit on the occupancy factor for a given atom in a given position?
What is the upper limit on the occupancy factor for a given atom in a given position?
Which refinement programs do not require that the occupancy factor be ≤ 1?
Which refinement programs do not require that the occupancy factor be ≤ 1?
Which parameter is used to describe the degree of order of an atom in protein crystallography?
Which parameter is used to describe the degree of order of an atom in protein crystallography?
What is the purpose of noncrystallographic symmetry (NCS) in refinement?
What is the purpose of noncrystallographic symmetry (NCS) in refinement?
How are NCS-related equivalent atoms superimposed in refinement?
How are NCS-related equivalent atoms superimposed in refinement?
Study Notes
Atomic Parameters in Model Building
- Each atom in a PDB file is assigned five parameters: X, Y, Z coordinates, occupancy, and B-factor.
- Occupancy: Indicates the percentage of symmetry-related atoms occupying a specific position, ranging from 0 to 1.
- B-factor: Reflects atomic mobility and order, with values typically varying from ~10 to ~100 Ų.
PDB File Format
- PDB files are text files that describe three-dimensional structures of molecules stored in the Protein Data Bank.
- Atomic models are characterized by numerous parameters essential for structural analysis.
Refinement of Papain Crystal Structure
- Papain crystal structure was refined at a resolution of 1.65 Ã…, encompassing:
- 25,000 independent reflections (diffraction spots).
- 8,000 parameters (X, Y, Z coordinates, B-factors) corresponding to 2,000 atoms, excluding hydrogen atoms.
- The observations-to-parameters ratio is only 3, indicating potential problems due to measurement errors in observations.
Geometry Information in Refinement
- Geometry data is integrated into the refinement process, incorporating:
- Bond lengths.
- Bond angles.
- Dihedral angles, established from small-molecule crystallography.
- Stereochemical Data: Utilized to enhance observational data:
- Constraints: Considered rigid, allowing only for variations in dihedral angles.
- Restraints: Allow variations but impose penalties for discrepancies, increasing refinement accuracy.
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Description
Test your knowledge on electron density maps and their calculation methods in this informative quiz. Learn about the relationship between observed structure factor amplitude and theoretical phases, as well as the potential biases that can arise in the calculated structure. Discover how the similarity between the phasing model and the unknown affects the accuracy of the calculated structure.
