First cycle
degree courses
Second cycle
degree courses
Single cycle
degree courses
School of Science
CHEMISTRY
Course unit
CRYSTALLOGRAPHY AND BIOCRYSTALLOGRAPHY
SC01123243, A.A. 2019/20

Information concerning the students who enrolled in A.Y. 2019/20

Information on the course unit
Degree course Second cycle degree in
CHEMISTRY
SC1169, Degree course structure A.Y. 2018/19, A.Y. 2019/20
N0
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Degree course track Common track
Number of ECTS credits allocated 6.0
Type of assessment Mark
Course unit English denomination CRYSTALLOGRAPHY AND BIOCRYSTALLOGRAPHY
Department of reference Department of Chemical Sciences
Mandatory attendance No
Language of instruction Italian
Branch PADOVA
Single Course unit The Course unit can be attended under the option Single Course unit attendance
Optional Course unit The Course unit can be chosen as Optional Course unit

Lecturers
Teacher in charge ROBERTO BATTISTUTTA CHIM/06

ECTS: details
Type Scientific-Disciplinary Sector Credits allocated
Core courses CHIM/06 Organic Chemistry 6.0

Course unit organization
Period Second semester
Year 1st Year
Teaching method frontal

Type of hours Credits Teaching
hours
Hours of
Individual study
Shifts
Lecture 6.0 48 102.0 No turn

Calendar
Start of activities 02/03/2020
End of activities 12/06/2020
Show course schedule 2019/20 Reg.2018 course timetable

Examination board
Board From To Members of the board
5 a.a. 2018/19 27/01/2014 30/11/2019 BATTISTUTTA ROBERTO (Presidente)
MAMMI STEFANO (Membro Effettivo)
ZANOTTI GIUSEPPE (Membro Effettivo)

Syllabus
Prerequisites: Basics of mathematics, physics and biological chemistry.
Target skills and knowledge: The course deals with the modern methodologies for the determination of the 3D atomic structure of small molecules, organic and inorganic, and of biological macromolecules by x-ray diffraction techniques on single crystals. The basics of diffraction and molecular structure determination will be presented, with particular emphasis on the most recent advances mainly in the field of macromolecular crystallography. Two other biophysical techniques for the structural characterization of macromolecules and their assemblies will be also presented, namely the electron cryo-microscopy (Cryo-EM) and the small-angle x-ray scattering (SAXS).
The course will benefit from examples of structure determination and analysis of relevant proteins, and from the guided reading of recent scientific papers on advanced topics.
Examination methods: Oral examination.
Assessment criteria: Comprehension of the course topics and capacity of utilization.
Course unit contents: Overview of crystallography: crystals, X-ray diffraction and the mathematics of crystallography. Crystallization: properties, growth and quality of crystals; crystallization techniques and strategies; crystallization of proteins.
Crystal geometry: periodic lattices and symmetry in 3D; space groups; reciprocal lattice and reciprocal space symmetry; systematic absences.
Diffraction basics: scattering of X-rays; atomic scattering factors, structure factor and B-factor; geometric principles of diffraction, Bragg law, Ewald sphere and Friedel pairs; anomalous scattering.
Instrumentation and data collection techniques: overview, data reduction.
From diffraction data to electron density: introduction; Fourier transform and diffraction; the phase problem; Patterson function and Patterson maps.
Experimental phasing: solving the phase problem; marker atom substructure methods; isomorphous replacement (MIR, SIR), anomalous scattering (SAD, MAD), SIRAS, direct methods, molecular replacement; improvement of phases, density modification techniques.
The resolution revolution: recent crucial advances in Cryo-EM. Comparison between x-ray crystallography and Cryo-EM.
Interaction of electrons with matter: principles of electron scattering and diffraction; transmission electron microscope (TEM) basic anatomy.
Image formation by amplitude contrast or phase contrast: TEM of biological specimens; weak-phase-object approximation for weak electron scatters; defocusing and lens aberrations for increasing contrast.
Fourier transform and image formation in TEM: point spread function (PSF) and contrast transfer function (CTF); single particle analysis; sample preparation.
From 2D images to the 3D structure: image reconstruction; resolution in crystallography and Cryo-EM.
Model building and refinement in X-ray crystallography and in Cryo-EM: principles and practice. Structure validation and analysis: quality of the final refined 3D models derived by X-ray crystallography and Cryo-EM.
Small Angle X-ray Scattering (SAXS) in structural biology: principle and basics; the SAXS experiment; scattering of particles in solution vs scattering in a crystal.
SAXS curves and particle shapes: Guinier plot and distance distribution function, radius of gyration and maximun particle size, Porod volume, Kratky plot for globular and unfolded proteins; interpolation of SAXS data with 3D protein models.
Examples of protein structure determination. Reading a protein structure paper.
Planned learning activities and teaching methods: Lessons and guided demonstrations.
Additional notes about suggested reading: Lesson slides.
Textbooks (and optional supplementary readings)
  • Bernhard Rupp, Biomolecular crystallography. New York: Garland Science, 2010. Cerca nel catalogo
  • Giacovazzo, Monaco, Artioli, Viterbo, Ferraris, Gilli, Zanotti, Catti, Fundamentals of Crystallography, 2nd Edition. Oxford: Oxford University Press, 2002. Cerca nel catalogo
  • Grant Jensen, Getting Started in Cryo-EM. --: --, --. http://cryo-em-course.caltech.edu

Innovative teaching methods: Teaching and learning strategies
  • Lecturing
  • Problem based learning
  • Case study
  • Interactive lecturing
  • Questioning
  • Problem solving
  • Concept maps
  • Use of online videos
  • Learning journal

Innovative teaching methods: Software or applications used

Sustainable Development Goals (SDGs)
Quality Education