1. Analysis of crystal structures
Preconsiderations
- Potential errors
- Missing regions
- Artifacts by crystal-packing
- Resolutions
Analysis of interactions
- Hydrogen bonds
- Hydrophobic interactions
- Salt bridges
- Surface charge representations
Dynamics or flexibility
- Temperature factor
- Loop? Turn?

2. Electron density of crystal is average of all molecules in crystal
Reality
ideal
Crystal
Electron density

3. Potential errors in crystal structures
Physical defects of crystals; damage of crystal in preparation, radiation damage during data collection
Mosaicity of crystal
Incompleteness of data
Inaccuracy of high resolution data; vibration or rotation of side chains
Result in bad electron density map

4. Physical defects of crystals
Damages in preparation
Melting
Breaking into single crystal
Uneven growth of crystal
Radiation damage

5. Incompleteness and inaccuracy of diffraction data
Blurred spot at high res.
Loss of low res. data by beam stopper

6. Crystal packing artifact
Different configuration of loop
In solution
In crystal

7. Resolution vs Rotamers of side chains
> 3.5Å
~ 2.8Å

8. Crystallographic data collection and structure refinement statistics
Rmeas (or Rsym); good as low
I/sigma; background to intensity ratio, >2 or 3
R-work; <0.2 at <2.0A, ~0.25 at ~2.5A,
<0.3 at >2.8 to 3.0A
R-free; R-work ~0.07 is appropriate
RMSD bond length; <0.01
RMSD bond angle; <1

9. Analysis of interactions
Tools
Visualization; Pymol, Coot
Analysis; CCP4, VADAR

10. Analysis of interaction
Hydrogen bonds
2.5 Å < distance between donor and acceptor < 3.5 Å
120° < angle N–O=C, etc., < 180°
In protein to water, only distance matters
Usually calculated by analysis program; ex.) VADAR

11. Analysis of interaction
Hydrophobic interaction
Non-real interaction; by exclusion of ordered water it increases net-entropy of system -> DG favorable
As strong as hydrogen bonding when hydrocarbons are enough
Shape complementary is a key to define (No distance or angle limit)

13. Analysis of interaction
Salt bridge
Electrostatic interaction between – (Glu, Asp) and + charged side chains (Lys, Arg)
Distance; <5A
Charge of each side chains must be head to head
In <3A distance, they occasionally makes hydrogen bond

14. Analysis of interaction
Surface charge representations
Net surface charge distribution of protein
Providing clue of binding sites in charge based interactions
Positive charge – blue
Negative charge - red

15. Flexibility of structure
turn
Scheme of turn
Loop

16. Dynamics
B-factor; temperature factor representing vibration of atom in temperature change