BCH 184 Crystallography Flashcards
What is contained in a PDB file?
A header and a list of atoms and coordinates
Why are X-rays used?
X-rays have a wavelength small enough to measure the atoms. (1-2 Angstroms)
Why are crystals used?
They have a repeating pattern
What makes a unit cell?
A unit lattice with a motif
3 properties of protein crystals?
Multiple crystalline forms, significant water content, Proteins retain functions in the crystal
How are crystals grown?
Using Vapor Diffusion by a slow, controlled precipitation from aqueous solution under conditions that do not denature the protein
What is Bragg’s Law?
What are the four methods for estimating Phases for individual a’ values?
- Molecular replacement
- Multiple Isomorphous Replacement (MIR)-multiple heavy atom derivitives
- Single Isomorphous Replacement with Anomalous Scattering (SIRAS)
- Multiwavelength Anomalous Dispertion (MAD)
How do we judge a structure Model?
Reflection data, Methods of phase estimation, Refinement Statistics (R-factor, R-Free), Protein Chemistry
Whats the equation for the R-Factor
Why do you need a crystalline array of protein in order to obtain a 3-D molecular model of that protein by X-ray crystallography (using present-day technology)?
The crystalline array means that the xray with have a projection based on a repeating pattern of the same molecular structure again and again. Affects like the phase interactions from Braggs law will cause the repetition of that pattern to create effects that amplify the refraction patterns of the molecules forming the crystal
Why is X-ray crystallography conducted with X-rays rather than with visible light rays?
X-rays are the range of electromagnetic radiation small enough to interact with the atoms of the molecules (around one angstrom)
Sometimes when a substrate analog is added to a protein crystal, the crystals shatter. Why?
If a substrate analog causes a conformational change in the macromolecule, then the repeating pattern formed by the crystalline state of the macromolecules would be completely disrupted by the shape changes.
What information is provided by the intensity of an individual reflection in a diffraction patter recorded in X-ray crystallography?
The miller incidences and eventually phase information depending on the type of diffraction test done
In x-ray crystallography, what is a structure factor? What are the primary components of a structure factors? What aspect of the structure factor can be recorded experimentally and what aspect cannot be recorded experimentally?
A structure factor is a mathematical function, a Fourier sum, describing the amplitude and phase of a wave diffracted from a crystal lattice plane characterized by miller indices, it contains amplitudes which can be measured experimentally and phases which must be determined through other methods like Molecular replacement, MIR, SIRAS, or MAD
explain this diagram
- Harker Diagram
a. This circle is from the a patterson diagram vector, is radius being the length of that vector
b. The second circle is the equivalent patterson diagram vector but from a diagram that includes a heavy metal ion, its displaced from the origin by the negative of the difference between the vectors (-F_h)
The two points the circles overlap are the two possible solutions for the phase angle of F_p
whats wrong with this diagram?
The positive region represents where there should be more electron density and the negative region represents where there should be less. The arginine structure should be mirrored across a diagonal (bottom left to top right) plane so that there is more atoms and thus more electron destiny in the positive region and less in the negative region.
