Jan 29 Flashcards
What kind of symmetry in diffraction pattern? Is it the same or diff from crystal symmetry?
It is point group symmetry. Crystal has symmetry so DP will show symmetry. They are diff as DP symmetry will have 1 point that stays in place, no translational symmetry in DP.
What are the 2 categories of X-ray sources?
X-ray generators and synchrotrons.
How do X-ray generators work, what are the 2 types?
Have filament that gives of electrons, then voltage creates electric field that pulls electrons towards the anode. X-ray tube will have anode with water to cool it, or can have rotating anode so surface has chance to cool down before hit again. These X rays pass through Beryllium window as it is solid and not very electron dense. Need solid window so can keep inside of generator under vacuum.
What are the 3 energy level relaxations given off to produce X-rays. What is the mechanism for this?
electron will kick out low level electron, so another from higher level will drop to fill the spot, producing x-ray. Have Ka1 and Ka2, similar energy elvels in 2P (L level). Then have KB from the 3P (M level).
What filter do we use to block what type of x-ray emmision before X-rays hit crystal?
Use nickel filter to absorb KB which is slightly shorter wavelength, doesn’t work as well as Kalpha emission. Our anode is copper that is hit by electrons, so we use nickel (beside it on periodic table) to block out the emission from it. We do this otherwise we get double the points in DP.
How synchrotron produce X-rays?
Bend electrons to give off X-rays
What is a goniometer?
It positions the crystal at diff angles as X-rays pass through it.
What would be a good element for beam stopper for x-rays?
Lead, it is electron dense
Caplillary vs cryoloop mounting of protein crystal?
Capillary will have tube with special glass filled with mother liquor, then from hanging drop put the drop on top of capillary, the crystal will sink to bottom of tube. Then remove most liquid and break of top of tube and seal it.
Cryoloop will scoop crystal out of solution, hold it as X-rays pass through it. Cold N2 blown over it to help proteins stay stable, but not freezing as ice will diffract xrays and damage crystal.
What is autoindexing?
It is when you take an image at 0 and 90 degrees of phi and take this image over +/- 1 degree. Then collect DP from each, and software will compare them and figure out possible unit cell shapes and orientation the unit cell is currently in
What is the penalty in autoindexing, does the lowest penalty mean the best unit cell option?
Not always best option. You get the abc lengths and alpha, beta, gamma angles. Lets say it predicts you could have tetragonal primitive (one of many). You would expect 90 degrees for each angle and expect 2 of the lengths to be equal. If it comes back with angles not 90 degrees and 2 side lengths that are sort of close but not really, then the penalty will be higher. You will also get poss spacegroups to pick from
How accurate is autoindexing for symmetry purposes?
It is geometric info, not measuring intensities of XRD pattern, so not symmetry info.
What is the number of measurable reflections?
It is when you have a limiting sphere with radius of 2/wavelength. Inside it you have sphere of reflection with radius of 1/wavelength. Using the volume of limiting sphere and volume of reciprocal unit cell, you can get number of measurable reflections based on the volume and wavelengths.
