Notes in Lecture 5

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Published	10/19/2024	3 ways to represent phasing: {{c1::Linear wave}} representation (variable: {{c2::\(\alpha\)}}, units: {{c3::0-2\(\pi\) radians}}){{c1::Circu…
Published	10/19/2024	RGB color wheel is red at {{c1::0}}º, green at {{c1::120}}º, and blue at {{c1::240}}º.
Published	10/19/2024	The {{c1::phase}} problem: no detector collects the {{c1::phase}}.
Published	10/19/2024	Detectors can detect {{c1::position}}, {{c1::wavelength}}, and {{c1::amplitude}}.
Published	10/19/2024	{{c1::Position}}: which matter plane produced the wave
Published	10/19/2024	{{c1::Wavelength}}: XRC x-rays are monochromatic single wavelength
Published	10/19/2024	{{c1::Amplitude}}: the overall contribution of that matter plane
Published	10/19/2024	Cystallographers solve {{c1::electron density}}, not structures. The structural models are then fit into the density using statistical (RMSD) methods.…
Published	10/19/2024	An XRC spot is a {{c1::structure}} factor. Each is unique to a single {{c2::Bragg plane}}, with a unique {{c2::phase}}
Published	10/19/2024	Structure factor phases are addressed by the {{c1::h, k, l}} values, which can also be seen as {{c2::frequencies}}; higher {{c1::h, k, l}} values are …
Published	10/19/2024	{{c1::Molecular replacement}} is not a de novo method, meaning it cannot be used for proteins for which there are no existing homology models.
Published	10/19/2024	The molecular replacement method uses a {{c1::mathematical triad}}, for which any two parts of the equation may be used to calculate the other.
Published	10/19/2024	{{c1::Phase refinement}}: cycling through the mathematical triad in molecular replacment.
Published	10/19/2024	The recursive application of the mathematical triad takes you from the {{c1::replacement (homology)}} model to the {{c1::new structure}}.
Published	10/19/2024	Protein crystals move enough to remain {{c1::enzymatically active}}.
Published	10/19/2024	The {{c1::solvent channels}} in the protein crystal are large enough that substrate molecules can permeate the crystal and reach the enzyme's active s…
Published	10/19/2024	If the {{c1::active site}} is open to the solvent channels and the {{c1::molecular motions}} of the enzymatic activity do not disrupt the crystal, the…
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