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Protein Structure Model, First Step, Third Step - Coggle Diagram

- - - - If protein crystal is able to retain its function; native structure
        
        Second step
      - By testing whether biological function of protein is retained
        
        Protein crystal is redissolved in buffer
        
        Enzymatic activity of redissolved protein crystal is compared with the activity level of the active protein sample
        
        Enzymatic activity level and function is the same, protein crystal has its native structure
        
        Enzymatic activity level and function is different, protein do not have native structure, purification and crystallization needs to be redone
- - - - Glycine
        
        R group of H offers very low stearic hindrance, allows the amino acid to occupy many spaces. No matter how big the other R groups are, there will be no stearic hindrance.
        Glycine would be found all over the Ramachandran plot, even in disallowed regions
      - Proline
        
        The ring structure in the proline obstructs phi angle rotation. Being unable to rotate, it would be found in a very specific region of the Ramachandran plot, which is the white region
- - - - Utilizes a X-ray tube which shines a beam of incident X-rays of specific wavelength onto the crystal.
        
        crystalline structure causes a beam of incident X-rays to diffract into many specific directions, forming diffraction patterns
        
        by measuring angles and intensities of these diffracted beams, the electron density map can be produced
        
        From this electron density, the mean positions of the atoms in the crystal can be determined, as well as their chemical bonds, and various other information.
  - - - Many nuclei have spin and all nuclei are electrically charged.
        
        In the presence of the magnetic field, the atoms (who have a net spin) are aligned.
        
        When an external magnetic field is applied, the energy transfer excites the nuclei causing its base energy to reach to a higher energy level - when the spin returns to its base level, energy is emitted.
        
        The energy transfer takes place at a specific wavelength that corresponds to radio frequencies
        
        The signal that matches this transfer is measured in many ways and processed in order to yield an NMR spectrum for the nucleus concerned.
        
        The chemical shift of atoms are analyzed in the NMR spectrum