Fan Lecture 7 Flashcards
What is structure refinement?
Minimize the difference between measured diffraction intensities and intensities predicted by the current model.
How does refinement happen?
More Fourier transformations = better resolution
As more structure factors are included in the Fourier sum, the electron density within the unit cell becomes resolved to higher resolution
How does refinement differ in real space vs reciprocal space?
Real space: operations to atomic coordinates
Reciprocal space: operations to improve phases
What is the free R-factor?
measures how well the current atomic model predicts a subset of the measured intensities that were not included in the refinement
What is used to calculate the free R-factor?
Control group: not used during refinement except for quality control and cross-validation
- small set of randomly chosen reflections (5% of the total)
Why do we use free R-factor?
provides a better and less-biased measure of the overall model performance
How does free r-factor compare to R?
R uses the entire data set that p roduced the model, while R-free uses those not in the refinement.
R-free is always larger than R.
How do you judge a structure model?
1) Reflection data
2) Methods of phase estimation
3) Refinement statistics
4) Protein chemistry
What are the 4 methods of phase estimations?
MIR, SIRAS, MAD, MR
What range can we estimate phases in?
10^3 to 10^5 individual a’hkl values required for calculating electron density
How is R-factor calculated?
Σ||Fo|-|Fc||/Σ|Fo|
What is a good range for R in a 2.5 angstrom model?
Less than 0.2 is good
0.12-0.14 is excellent
What are other factors besides x, y, z in the title of the PDB file?
B-factor: temperature, a measure of how much oscillation around the position
Occupancy: measure of each atom whether it occupies the position specified
What is the full title format for PDB file?
atom x,y,z n b
atom position occupancy temperature
What is RasTop?
Open source graphic software to manipulate macromolecule coordinates
