36 Questions
Which method is used to calculate the electron density map?
Observed structure factor amplitude
Which component provides more structural information in the calculation of the electron density map?
Theoretical phases
Which statement is true about the bias in the calculated structure?
The bias in the calculated structure depends on the similarity between the phasing model and the unknown
Which method can be used to treat the model bias problem in molecular replacement?
Calculate a composite omit map
What is the expected outcome of using a poly-alanine model for molecular replacement?
Side chain should emerge if phases are sufficiently accurate
What should the resulting map from a composite omit map calculation contain?
Only signal from the unknown structure
Which unit cell has a 5-fold NCS in this example?
P2
What needs to be defined in order to apply NCS averaging?
The mask
Which parameter describes the degree of order of an atom?
B factor
What is the range of values for the occupancy parameter?
0 to 1
How many parameters are assigned to every atom in the PDB file generated by model building?
5
Atomic models contain a large number of ______
parameters
Inclusion of stereochemical data significantly increase the number of ______
observations
_______ can be applied in two different ways
stereochemical data
Which file format describes the three-dimensional structures of molecules in the Protein Data Bank?
PDB file
What is the ratio of observations to parameters in the refinement process of the papain crystal structure?
3
What type of data significantly increases the number of observations in the refinement process?
Stereochemical data
How are stereochemical data applied in the refinement process?
As restraints
What parameters are assigned to every atom in the PDB file generated by model building?
X, Y, Z, B
Which degrees of freedom are minimized for each group of atoms specified as a rigid body?
Both rotational and translational degrees of freedom
What is the purpose of rigid body refinement in the early stages of refinement?
To improve the ratio of parameters to observables
How can the entire model be treated in rigid body refinement?
Both as a rigid body and as linked, rigid groups
Which technique is commonly used for finding the best fit of the model to the data in protein crystallography?
Least-squares optimization
What is the purpose of position refinement in protein crystallography?
To refine the atomic position parameters
Which parameter is fixed to ideal values in torsional refinement?
Bond angles
What does torsional refinement reduce in the refinement process?
Parameters
In torsional refinement, atoms are grouped into what?
Rigid bodies
Which factor is indicated by high B-values in protein crystallography?
Atomic mobility
What does the B-factor relate to in protein crystallography?
Thermal motion
What does a high B-factor value suggest in protein crystallography?
Low atomic mobility
Which factor is used to describe disorder in the model?
Occupancy factor
What is the upper limit on the occupancy factor for a given atom in a given position?
1
Which refinement programs do not require that the occupancy factor be ≤ 1?
Some refinement programs
Which parameter is used to describe the degree of order of an atom in protein crystallography?
B-factor
What is the purpose of noncrystallographic symmetry (NCS) in refinement?
To reduce the number of parameters
How are NCS-related equivalent atoms superimposed in refinement?
Through a rotation and translation operator
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.
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