X-ray Crystallography BMB/Bi/Ch173 02/06/2017
|
|
- Clifton Houston
- 6 years ago
- Views:
Transcription
1 1. Purify your protein 2. Crystallize protein 3. Collect diffraction data 4. Get experimental phases 5. Generate an electron density map 6. Build a model 7. Refine the model 8. Publish X-ray Crystallography BMB/Bi/Ch173 02/06/2017 Catalysis-dependent selenium incorporation and migration in the nitrogenase active site iron-molybdenum cofactor Spatzal, Perez, Howard & Rees elife 2015 Petsko and Ringe
2 Pauling s September 1953 Protein Conference in Pasadena Max Perutz, Vernon Shomaker, James Watson, Jack Dunitz, Julian Huxley, Francis Crick, Richard Marsh, Ken Trueblood, Maurice Huggins, Ray Pepinsky, Ken Palmer, John Rollet, Vitorio Luzzati, George Beadle, David Davies, Maurice Wilkins, John Kendrew, Alex Rich, Bea Magdoff, Maurry King, Linus Pauling, Robert Corey, David Harker, William Astbury, Richard Bear, William Bragg, Lindo Patterson, John Edsall, Francis O. Schmidt, John Randall, Barbara Low, I.F. Trotter
3 Satellite Tobacco Mosaic Virus (STMV) Crystal MacPherson
4
5
6 Useful texts and links Rhodes Crystallography made crystal clear Drenth Principles of protein X-ray crystallography Lattman & Loll Protein crystallography: a concise guide MacPherson Preparation and analysis of protein crystals Ed. Rossmann & Arnold Crystallography of biological macromolecules: volume F Bernhard Rupp Biomolecular Crystallography
7 Nobel prizes related to X-ray Crystallography 1901 Physics (1 st ) Röntgen X-rays 1905 Physics von Lenard cathode rays 1914 Physics von Laue X-ray diffraction by crystals 1915 Physics Bragg & Bragg first crystal structure 1946 Chemistry Sumner First enzyme crystals 1962 Chemistry Perutz & Kendrew First protein structure 1962 Medicine Watson, Crick & Wilkins DNA structure 1964 Chemistry Hodgkin Protein crystallography 1976 Chemistry Lipscomb Borane structure (Rees mentor) 1982 Chemistry Klug Crystallographic EM 1985 Chemistry Hauptman & Karle Direct methods (Isabella credited) 1988 Chemistry Deisenhofer, Huber & Michel Photosynthetic reaction center 1997 Chemistry Agre & Walker F1 ATPase structure, aquaporins 2003 Chemistry MacKinnon Ion channel structures 2006 Chemistry Kornberg RNA polymerase structure 2009 Chemistry Ramakrishnan, Steitz and Yonath Ribosome structures 2012 Chemistry Leftkowitz & Kobilka - GPCRs
8 The international year of crystallography (2014)
9 X-ray crystallography Why X-rays? Right wavelength to resolve atoms Why crystal? Immobilize protein, enhance weak signal from scattering What is a protein crystal? Large solvent channels 20-80% solvent Same density as cytoplasm Are crystal structures valid compared with solution structures? Enzymes active in crystals Usually -- Compare NMR and x-ray structures Structures correlate with biological function Multiple crystal forms look same -- small effects of packing (flexible hinges can differ depending on packing)
10 Crystal lattices and symmetry y A crystal is a regular, 3-dimensional repeating array. The fundamental building block is the unit cell The crystal is built up by translations along x, y and z (which are not necessarily orthogonal) x z Note that x, y, z form a right-handed coordinate system
11 Unit cell Described by three vectors, a, b, and c, which are related by angles α, β and γ Lattice built up by translating the unit cell along each of the lattice vectors
12 Choice of unit cell Criteria for choosing a unit cell: There are many different cell choices for a lattice; I, II and III all constitute unit cells from which the entire lattice can be generated 1. Right-handed axis system 2. The basis vectors should coincide as much as possible with directions of highest symmetry 3. Cell should be smallest one that satisfies previous condition. This may mean the choice of a non-primitive unit cell. 4. a > b > c 5. Angles either all <90 or 90
13 Primitive and non-primitive unit cells Primitive cells have a single point in each unit cell (1/8 of each corner point) Non-primitive cells have more than one point in each unit cell
14 Contents of a unit cell A unit cell does not have to contain a full object but it must contain the sum of the repeating object The contents of a unit cell can have no intrinsic symmetry, or can contain objects related by symmetry operations.
15 Space filling repeats Forms closed lattice Can t fill 5-fold 2-fold 3-fold 7-fold 8-fold 4-fold 6-fold
16 Symmetry operations (2 1 )screw axis m n The symmetry operator m: rotate 360 o /m along an axis to unit cell plane The screw axis m n rotate 360 o /m along an axis to unit cell plane translate n/m along unit cell Crystallographic symmetry operations describe the symmetry of the unit cell as well as of the entire crystal. Symmetry of 5 or >6 cannot be used to build a 3-dimensional lattice therefore they do not exist except in local symmetry
17 Examples of screw axis Rotate 360/m = 120 Translate n/m n/m unit cells = 1/3 360/m = 120 n/m unit cells = 2/3 360/m = 60 n/m unit cells = 1/6
18 Biological systems are limited in symmetry Mirror Plane Biological systems are chiral and can t generate mirror planes or inversion centers. Inversion center
19 Point groups in proteins
20 Space groups Crystal System Bravais Type Condition of geometry Triclinic P None 1 Minimum symmetry a complete description of a crystal lattice defines a unit cell type a set of symmetry operations 230 possible 3D space groups only 65 biological space groups due to chirality (no mirror or inversion centers) Crystal systems define classes of space groups Higher symmetry means less data needed for completeness but more molecules in the unit cell (larger cells ) Monoclinic P, C α=γ= fold parallel to b Orthrombic P, I, F α=β=γ=90 Three 2-folds Tetragonal P, I a=b; α=β=γ= fold parallel to c Trigonal P, R Hex: a=b; α=β=90; γ=120 Rhomb: a=b=c; α=β=γ 1 3-fold axis Hexagonal P a=b; α=β=90; γ= fold axis Cubic P, F, I a=b=c; α=β=γ= folds along diagonal Defined in excruciating detail in The International Tables for Crystallography volume A
21 65 biological space groups Lot s of possible space groups P and P2 1 most common Least restrictive packing Triclinic P 1 Monoclinic P 2 P 21 C 2 Orthorhombic P P P P C C F I I Tetragonal P 4 P 41 P 42 P 43 I 4 I 41 P P P P P P P P I I Trigonal P 3 P 31 P 32 R 3 P P P P P P R 3 2 Hexagonal P 6 P 61 P 65 P 62 P 64 P 63 P P P P P P Cubic P 2 3 F 2 3 I 2 3 P 21 3 I 21 3 P P F F I P P I Wuckovic & Yeates (1995) NSB 2(12) 1062
22 Space groups Space groups define internal symmetry Given the space group and cell dimensions one can construct a unit cell Space group defines relationship of molecules P (19) Laue class mmm Orthrombic 4 Transformations X, Y, Z ½+X, ½-Y, -Z -X, ½+Y, ½-Z ½-X, -Y, ½+Z P (152) Laue class -3m1 Trigonal 6 Transformations X, Y, Z -Y, X-Y, ⅓+Z -X+Y, -X, ⅔+Z Y, X, -Z X-Y, -Y, ⅔-Z -X, -X+Y, ⅓-Z
23 The asymmetric unit P2 a a.u. 2-fold axis b a.u. The asymmetric unit is the smallest fraction of the unit cell lacking internal symmetry The unit cell can be built up by applying symmetry operations to the asymmetric unit Unit cell
24 MacPherson
25 Joseph Fourier Théorie analytique de la chaleur The observation: a periodic function can be described as the sum of simple sine and cosine functions that have wavelengths as integrals of the function Also first predicted the Greenhouse Effect
26 Fourier Series A set of functions from a Fourier synthesis that can be summed to reproduce a periodic function f (x) = F cos2π(hx + α) s(t) cos2π(x) 1 cos2π(3x) 3 t 1 cos2π(5x) 5 Rhodes Crystallography Made Crystal Clear
27 Fourier Series of atoms f (x) = F cos2π(hx + α) A set of functions from a Fourier synthesis that can be summed to reproduce a periodic function C C O
28 How can we describe the diffraction pattern of a protein in a crystal? Because there is no lens to refocus x-rays, we have to understand reciprocal space. Diffraction: Scattering followed by interference
29 Diffraction by a wave Diffraction: deviation of light from rectilinear propagation, is a characteristic of wave phenomena which occurs when a portion of a wave front is obstructed in some way. When various portions of a wave front propagate past some obstacle, and interfere at a later point past the obstacle, the pattern formed is called a diffraction pattern. Obstruction (slit) is smaller than the wavelength
30 Diffraction pattern With 2 slits you now get patterns of interference. -Constructive when peaks or troughs intersect -Destructructive when peaks and troughs intersect.
31 Convolution theorem The FT of the convolution of two functions is the product of their FTs The diffraction pattern of a lattice is a lattice The diffraction pattern of a molecular crystal product of the transform of the molecule (molecular transform) the diffraction pattern of a lattice (reciprocal lattice) Sampling of molecular transform at reciprocal lattice points
32 The convolution of two functions
33 Convolution theorem Diffraction pattern of a set of lines is a row of dots perpendicular to the lines The separation between the dots is proportional to the inverse of the separation between the lines Form lattice by multiplying the two functions The diffraction pattern of the lattice is a convolution of the diffraction patterns of the two sets of lines
34 All of the lens contributes to each point
35
36 Fourier transforms
37 Laser fun Red, Blue, Green Wavelength Red>Green>Blue ROYGBIV Red 650nm, Green 530nm, Blue 405nm 1mW, 5mW, 10mW 50 µm vs 100 µm mesh
38
39 The transform of the convolution of two functions is the product of the transforms a b * = Fourier transform of this F.T. F.T. F.T. x = = this F.T.(a b)
40 Same molecular transform sampled by different lattices a) Molecular transform b) Lattice c) Convolution of lattice and transform d - f ) Same molecular transform sampled by different lattices Modified from Lipson & Taylor, 1964
41 Diffraction from an atom e - diffract X-rays Can be described by an approximation of the scattering by the electron shell An atom diffracts x- rays in all directions
42 When do we get a diffraction pattern? When we get constructive interference from two diffracted waves Bragg s Law nλ = 2d sinθ
43 Diffraction planes reflect X-rays λ d θ θ θ Bragg s Law nλ = 2dsinθ
44 λ Bragg s Law d θ θ λ θ d λ θ θ 2dsinθ The difference in travel is equal to a multiple of the wavelength. All of the atoms close to the Bragg plane contribute to the diffraction nλ = 2dsinθ
45 Lattice planes (2 1 0) plane (1 3 0) plane Plane defined by ( a h, b k, c l ) Can have negative integers
46 Getting to reciprocal space 1/d 1 1/d 2 θ 1 θ 2 d 1 d 2 The angle that satisfies Bragg s law is inversely proportional to the lattice spacing Reciprocal space can be defined by a vector normal to the real plane giving us the reciprocal lattice d = nλ 2sinθ
47 Constructing the reciprocal lattice J.D. Bernal (1926) On the interpretation of X-ray, Single Crystal, Rotation Photographs Proceedings of the Royal Society 113:117 When do planes diffract? Rhodes Crystallography Made Crystal Clear
48 Ewald Sphere Diffracted X-ray 1/λ 1/d θ 1/λ θ θ Reciprocal lattice origin Crystal origin A construction to indicate which Bragg planes diffract for a given orientation 1 2d = 1 λ sinθ
Methods in Chemistry III Part 1 Modul M.Che.1101 WS 2010/11 1 Modern Methods of Inorganic Chemistry Mi 10:15-12:00, Hörsaal II George Sheldrick
Methods in Chemistry III Part 1 Modul M.Che.1101 WS 2010/11 1 Modern Methods of Inorganic Chemistry Mi 10:15-12:00, Hörsaal II George Sheldrick gsheldr@shelx.uni-ac.gwdg.de Part 1. Crystal structure determination
More informationLecture 1. Introduction to X-ray Crystallography. Tuesday, February 1, 2011
Lecture 1 Introduction to X-ray Crystallography Tuesday, February 1, 2011 Protein Crystallography Crystal Structure Determination in Principle: From Crystal to Structure Dr. Susan Yates Contact Information
More informationThe structure of liquids and glasses. The lattice and unit cell in 1D. The structure of crystalline materials. Describing condensed phase structures
Describing condensed phase structures Describing the structure of an isolated small molecule is easy to do Just specify the bond distances and angles How do we describe the structure of a condensed phase?
More informationX-ray analysis. 1. Basic crystallography 2. Basic diffraction physics 3. Experimental methods
X-ray analysis 1. Basic crystallography 2. Basic diffraction physics 3. Experimental methods Introduction Noble prizes associated with X-ray diffraction 1901 W. C. Roentgen (Physics) for the discovery
More informationOverview - Macromolecular Crystallography
Overview - Macromolecular Crystallography 1. Overexpression and crystallization 2. Crystal characterization and data collection 3. The diffraction experiment 4. Phase problem 1. MIR (Multiple Isomorphous
More informationCrystallographic Symmetry. Jeremy Karl Cockcroft
Crystallographic Symmetry Jeremy Karl Cockcroft Why bother? To describe crystal structures Simplifies the description, e.g. NaCl structure Requires coordinates for just 2 atoms + space group symmetry!
More informationIntroduction. Chem 6850/8850 X-ray Crystallography The University of Toledo.
Introduction Chem 6850/8850 X-ray Crystallography The University of Toledo cora.lind@utoledo.edu Course Goals To develop an understanding of basic crystallographic concepts - Helpful if you ever need to
More informationProtein Crystallography. Mitchell Guss University of Sydney Australia
Protein Crystallography Mitchell Guss University of Sydney Australia Outline of the talk Recap some basic crystallography and history Highlight the special requirements for protein (macromolecular) structure
More informationBasic Crystallography Part 1. Theory and Practice of X-ray Crystal Structure Determination
Basic Crystallography Part 1 Theory and Practice of X-ray Crystal Structure Determination We have a crystal How do we get there? we want a structure! The Unit Cell Concept Ralph Krätzner Unit Cell Description
More informationCrystallography Reading: Warren, Chapters 2.1, 2.2, 2.6, 8 Surface symmetry: Can be a clue to underlying structure. Examples:
Crystallography Reading: Warren, Chapters 2.1, 2.2, 2.6, 8 Surface symmetry: Can be a clue to underlying structure. Examples: Snow (SnowCrystals.com) Bismuth (Bao, Kavanagh, APL 98 66103 (2005) Hexagonal,
More informationHelpful resources for all X ray lectures Crystallization http://www.hamptonresearch.com under tech support: crystal growth 101 literature Spacegroup tables http://img.chem.ucl.ac.uk/sgp/mainmenu.htm Crystallography
More informationApplications of X-ray and Neutron Scattering in Biological Sciences: Symmetry in direct and reciprocal space 2012
Department of Drug Design and Pharmacology Applications of X-ray and Neutron Scattering in Biological Sciences: Symmetry in direct and reciprocal space 2012 Michael Gajhede Biostructural Research Copenhagen
More informationScattering and Diffraction
Scattering and Diffraction Andreas Kreyssig, Alan Goldman, Rob McQueeney Ames Laboratory Iowa State University All rights reserved, 2018. Atomic scale structure - crystals Crystalline materials... atoms
More informationPX-CBMSO Course (2) of Symmetry
PX-CBMSO Course (2) The mathematical description of Symmetry y PX-CBMSO-June 2011 Cele Abad-Zapatero University of Illinois at Chicago Center for Pharmaceutical Biotechnology. Lecture no. 2 This material
More informationPhysical Chemistry I. Crystal Structure
Physical Chemistry I Crystal Structure Crystal Structure Introduction Crystal Lattice Bravis Lattices Crytal Planes, Miller indices Distances between planes Diffraction patters Bragg s law X-ray radiation
More informationSymmetry Crystallography
Crystallography Motif: the fundamental part of a symmetric design that, when repeated, creates the whole pattern In 3-D, translation defines operations which move the motif into infinitely repeating patterns
More informationFundamentals of X-ray diffraction
Fundamentals of X-ray diffraction Elena Willinger Lecture series: Modern Methods in Heterogeneous Catalysis Research Outline History of X-ray Sources of X-ray radiation Physics of X-ray scattering Fundamentals
More informationX-ray, Neutron and e-beam scattering
X-ray, Neutron and e-beam scattering Introduction Why scattering? Diffraction basics Neutrons and x-rays Techniques Direct and reciprocal space Single crystals Powders CaFe 2 As 2 an example What is the
More informationSOLID STATE 18. Reciprocal Space
SOLID STATE 8 Reciprocal Space Wave vectors and the concept of K-space can simplify the explanation of several properties of the solid state. They will be introduced to provide more information on diffraction
More informationChem 728 Introduction to Solid Surfaces
Chem 728 Introduction to Solid Surfaces Solids: hard; fracture; not compressible; molecules close to each other Liquids: molecules mobile, but quite close to each other Gases: molecules very mobile; compressible
More informationUNIT I SOLID STATE PHYSICS
UNIT I SOLID STATE PHYSICS CHAPTER 1 CRYSTAL STRUCTURE 1.1 INTRODUCTION When two atoms are brought together, two kinds of forces: attraction and repulsion come into play. The force of attraction increases
More informationChap 3 Scattering and structures
Chap 3 Scattering and structures Dept of Phys M.C. Chang Von Laue was struck in 1912 by the intuition that X-ray might scatter off crystals in the way that ordinary light scatters off a diffraction grating.
More informationProtein Structure Determination. Part 1 -- X-ray Crystallography
Protein Structure Determination Part 1 -- X-ray Crystallography Topics covering in this 1/2 course Crystal growth Diffraction theory Symmetry Solving phases using heavy atoms Solving phases using a model
More informationIntroduction to crystallography The unitcell The resiprocal space and unitcell Braggs law Structure factor F hkl and atomic scattering factor f zθ
Introduction to crystallography The unitcell The resiprocal space and unitcell Braggs law Structure factor F hkl and atomic scattering factor f zθ Introduction to crystallography We divide materials into
More informationResolution: maximum limit of diffraction (asymmetric)
Resolution: maximum limit of diffraction (asymmetric) crystal Y X-ray source 2θ X direct beam tan 2θ = Y X d = resolution 2d sinθ = λ detector 1 Unit Cell: two vectors in plane of image c* Observe: b*
More information3.012 Structure An Introduction to X-ray Diffraction
3.012 Structure An Introduction to X-ray Diffraction This handout summarizes some topics that are important for understanding x-ray diffraction. The following references provide a thorough explanation
More informationCrystals, X-rays and Proteins
Crystals, X-rays and Proteins Comprehensive Protein Crystallography Dennis Sherwood MA (Hons), MPhil, PhD Jon Cooper BA (Hons), PhD OXFORD UNIVERSITY PRESS Contents List of symbols xiv PART I FUNDAMENTALS
More information5 Symmetries and point group in a nut shell
30 Phys520.nb 5 Symmetries and point group in a nut shell 5.1. Basic ideas: 5.1.1. Symmetry operations Symmetry: A system remains invariant under certain operation. These operations are called symmetry
More informationCrystal planes. Neutrons: magnetic moment - interacts with magnetic materials or nuclei of non-magnetic materials. (in Å)
Crystallography: neutron, electron, and X-ray scattering from periodic lattice, scattering of waves by periodic structures, Miller indices, reciprocal space, Ewald construction. Diffraction: Specular,
More informationn-dimensional, infinite, periodic array of points, each of which has identical surroundings.
crystallography ll Lattice n-dimensional, infinite, periodic array of points, each of which has identical surroundings. use this as test for lattice points A2 ("bcc") structure lattice points Lattice n-dimensional,
More informationHandout 7 Reciprocal Space
Handout 7 Reciprocal Space Useful concepts for the analysis of diffraction data http://homepages.utoledo.edu/clind/ Concepts versus reality Reflection from lattice planes is just a concept that helps us
More informationThe Reciprocal Lattice
59-553 The Reciprocal Lattice 61 Because of the reciprocal nature of d spacings and θ from Bragg s Law, the pattern of the diffraction we observe can be related to the crystal lattice by a mathematical
More informationUnderstanding Single-Crystal X-Ray Crystallography Exercises and Solutions
Understanding Single-Crystal X-Ray Crystallography Exercises and Solutions Dennis W. Bennett Department of Chemistry and Biochemistry University of Wisconsin-Milwaukee Chapter Crystal Lattices. The copper
More informationChemical Crystallography
Chemical Crystallography Prof Andrew Goodwin Michaelmas 2014 Recap: Lecture 1 Why does diffraction give a Fourier transform? k i = k s = 2π/λ k i k s k i k s r l 1 = (λ/2π) k i r l 2 = (λ/2π) k s r Total
More informationLattice (Sieć) A collection of nodes, i.e. points with integral coordinates. In crystallography, a lattice is an
Prof. dr hab. Mariusz Jaskólski GLOSSARYUSZ TERMINÓW KRYSTALOGRAFICZNYCH (dla osób nie znających jeszcze krystalografii, ale znających język angielski) Symmetry (Symetria) Property of physical and mathematical
More informationGeneral theory of diffraction
General theory of diffraction X-rays scatter off the charge density (r), neutrons scatter off the spin density. Coherent scattering (diffraction) creates the Fourier transform of (r) from real to reciprocal
More informationTranslational symmetry, point and space groups in solids
Translational symmetry, point and space groups in solids Michele Catti Dipartimento di Scienza dei Materiali, Universita di Milano Bicocca, Milano, Italy ASCS26 Spokane Michele Catti a = b = 4.594 Å; Å;
More informationMolecular Biology Course 2006 Protein Crystallography Part I
Molecular Biology Course 2006 Protein Crystallography Part I Tim Grüne University of Göttingen Dept. of Structural Chemistry November 2006 http://shelx.uni-ac.gwdg.de tg@shelx.uni-ac.gwdg.de Overview Overview
More informationCrystallography past, present and future
Crystallography past, present and future Jenny P. Glusker Philadelphia, PA, U. S. A. International Year of Crystallography UNESCO, Paris, France 20 January 2014 QUARTZ CRYSTALS Quartz crystals found growing
More informationPhys 460 Describing and Classifying Crystal Lattices
Phys 460 Describing and Classifying Crystal Lattices What is a material? ^ crystalline Regular lattice of atoms Each atom has a positively charged nucleus surrounded by negative electrons Electrons are
More informationProbing Atomic Crystals: Bragg Diffraction
1 Probing Atomic Crystals: Bragg Diffraction OBJECTIVE: To learn how scientists probe the structure of solids, using a scaled-up version of X-ray Diffraction. APPARATUS: Steel ball "crystal", microwave
More informationPOINT SYMMETRY AND TYPES OF CRYSTAL LATTICE
POINT SYMMETRY AND TYPES OF CRYSTAL LATTICE Abdul Rashid Mirza Associate Professor of Physics. Govt. College of Science, wahdatroad, Lahore. 1 WHAT ARE CRYSTALS? The word crystal means icy or frozen water.
More information1/2, 1/2,1/2, is the center of a cube. Induces of lattice directions and crystal planes (a) Directions in a crystal Directions in a crystal are
Crystallography Many materials in nature occur as crystals. Examples include the metallic elements gold, copper and silver, ionic compounds such as salt (e.s. NaCl); ceramics, rutile TiO2; and nonmetallic
More informationSymmetry. 2-D Symmetry. 2-D Symmetry. Symmetry. EESC 2100: Mineralogy 1. Symmetry Elements 1. Rotation. Symmetry Elements 1. Rotation.
Symmetry a. Two-fold rotation = 30 o /2 rotation a. Two-fold rotation = 30 o /2 rotation Operation Motif = the symbol for a two-fold rotation EESC 2100: Mineralogy 1 a. Two-fold rotation = 30 o /2 rotation
More information2. Diffraction as a means to determine crystal structure
Page 1 of 22 2. Diffraction as a means to determine crystal structure Recall de Broglie matter waves: 2 p h E = where p = 2m λ h 1 E = ( ) 2m λ hc E = hυ = ( photons) λ ( matter wave) He atoms: [E (ev)]
More information31. Diffraction: a few important illustrations
31. Diffraction: a few important illustrations Babinet s Principle Diffraction gratings X-ray diffraction: Bragg scattering and crystal structures A lens transforms a Fresnel diffraction problem into a
More informationSolid State Physics Lecture 3 Diffraction and the Reciprocal Lattice (Kittel Ch. 2)
Solid State Physics 460 - Lecture 3 Diffraction and the Reciprocal Lattice (Kittel Ch. 2) Diffraction (Bragg Scattering) from a powder of crystallites - real example of image at right from http://www.uni-wuerzburg.de/mineralogie/crystal/teaching/pow.html
More informationNove fizickohemijske metode. Ivana Radosavljevic Evans Durham University, UK
Nove fizickohemijske metode Ivana Radosavljevic Evans Durham University, UK Nove fizickohemijske metode: Metode zasnovane na sinhrotronskom zracenju Plan predavanja: Difrakcione metode strukturne karakterizacije
More informationX-Ray structure analysis
X-Ray structure analysis Kay Diederichs kay.diederichs@uni-konstanz.de Analysis of what? Proteins ( /ˈproʊˌtiːnz/ or /ˈproʊti.ɨnz/) are biochemical compounds consisting of one or more polypeptides typically
More informationFourier Syntheses, Analyses, and Transforms
Fourier Syntheses, Analyses, and Transforms http://homepages.utoledo.edu/clind/ The electron density The electron density in a crystal can be described as a periodic function - same contents in each unit
More information2. Diffraction as a means to determine crystal structure
2. Diffraction as a means to determine crystal structure Recall de Broglie matter waves: He atoms: [E (ev)] 1/2 = 0.14 / (Å) E 1Å = 0.0196 ev Neutrons: [E (ev)] 1/2 = 0.28 / (Å) E 1Å = 0.0784 ev Electrons:
More informationAnalytical Methods for Materials
Analytical Methods for Materials Lesson 15 Reciprocal Lattices and Their Roles in Diffraction Studies Suggested Reading Chs. 2 and 6 in Tilley, Crystals and Crystal Structures, Wiley (2006) Ch. 6 M. DeGraef
More informationTILES, TILES, TILES, TILES, TILES, TILES
3.012 Fund of Mat Sci: Structure Lecture 15 TILES, TILES, TILES, TILES, TILES, TILES Photo courtesy of Chris Applegate. Homework for Fri Nov 4 Study: Allen and Thomas from 3.1.1 to 3.1.4 and 3.2.1, 3.2.4
More informationLecture 2 Symmetry in the solid state -
Lecture 2 Symmetry in the solid state - Part II: Crystallographic coordinates and Space Groups. 1 Coordinate systems in crystallography and the mathematical form of the symmetry operators 1.1 Introduction
More informationBasic Crystallography Part 1. Theory and Practice of X-ray Crystal Structure Determination
Basic Crystallography Part 1 Theory and Practice of X-ray Crystal Structure Determination Course Overview Basic Crystallography Part 1 n Introduction: Crystals and Crystallography n Crystal Lattices and
More informationSolid State Physics 460- Lecture 5 Diffraction and the Reciprocal Lattice Continued (Kittel Ch. 2)
Solid State Physics 460- Lecture 5 Diffraction and the Reciprocal Lattice Continued (Kittel Ch. 2) Ewald Construction 2θ k out k in G Physics 460 F 2006 Lect 5 1 Recall from previous lectures Definition
More informationX-Ray Scattering Studies of Thin Polymer Films
X-Ray Scattering Studies of Thin Polymer Films Introduction to Neutron and X-Ray Scattering Sunil K. Sinha UCSD/LANL Acknowledgements: Prof. R.Pynn( Indiana U.) Prof. M.Tolan (U. Dortmund) Wilhelm Conrad
More informationWhat use is Reciprocal Space? An Introduction
What use is Reciprocal Space? An Introduction a* b* x You are here John Bargar 5th Annual SSRL Workshop on Synchrotron X-ray Scattering Techniques in Materials and Environmental Sciences June 1-3, 2010
More informationX-ray Crystallography
2009/11/25 [ 1 ] X-ray Crystallography Andrew Torda, wintersemester 2009 / 2010 X-ray numerically most important more than 4/5 structures Goal a set of x, y, z coordinates different properties to NMR History
More informationDavid Martin Challenges in High Precision Beamline Alignment at the ESRF FIG Working Week Christchurch New Zealand 2016
Presented at the FIG Working Week 2016, May 2-6, 2016 in Christchurch, New Zealand David Martin Challenges in High Precision Beamline Alignment at the ESRF FIG Working Week Christchurch New Zealand 2016
More informationIntroduction to Materials Science Graduate students (Applied Physics)
Introduction to Materials Science Graduate students (Applied Physics) Prof. Michael Roth Chapter Reciprocal Lattice and X-ray Diffraction Reciprocal Lattice - 1 The crystal can be viewed as made up of
More informationCondensed Matter Physics Prof. G. Rangarajan Department of Physics Indian Institute of Technology, Madras
Condensed Matter Physics Prof. G. Rangarajan Department of Physics Indian Institute of Technology, Madras Lecture - 03 Symmetry in Perfect Solids Worked Examples Stated without prove to be in the lecture.
More informationGeometry of Crystal Lattice
0 Geometry of Crystal Lattice 0.1 Translational Symmetry The crystalline state of substances is different from other states (gaseous, liquid, amorphous) in that the atoms are in an ordered and symmetrical
More informationWe need to be able to describe planes and directions.
We need to be able to describe planes and directions. Miller Indices & XRD 1 2 Determining crystal structure and identifying materials (B) Plastic deformation Plastic deformation and mechanical properties
More informationPSD '17 -- Xray Lecture 5, 6. Patterson Space, Molecular Replacement and Heavy Atom Isomorphous Replacement
PSD '17 -- Xray Lecture 5, 6 Patterson Space, Molecular Replacement and Heavy Atom Isomorphous Replacement The Phase Problem We can t measure the phases! X-ray detectors (film, photomultiplier tubes, CCDs,
More information3.012 Fund of Mat Sci: Structure Lecture 18
3.012 Fund of Mat Sci: Structure Lecture 18 X-RAYS AT WORK An X-ray diffraction image for the protein myoglobin. Source: Wikipedia. Model of helical domains in myoglobin. Image courtesy of Magnus Manske
More informationX-ray Crystallography. Kalyan Das
X-ray Crystallography Kalyan Das Electromagnetic Spectrum NMR 10 um - 10 mm 700 to 10 4 nm 400 to 700 nm 10 to 400 nm 10-1 to 10 nm 10-4 to 10-1 nm X-ray radiation was discovered by Roentgen in 1895. X-rays
More informationCHEM-E5225 :Electron Microscopy. Diffraction 1
CHEM-E5225 :Electron Microscopy Diffraction 1 2018-10-15 Yanling Ge Text book: Transmission electron microscopy by David B Williams & C. Barry Carter. 2009, Springer Outline Diffraction in TEM Thinking
More informationProtein Crystallography
Protein Crystallography Part II Tim Grüne Dept. of Structural Chemistry Prof. G. Sheldrick University of Göttingen http://shelx.uni-ac.gwdg.de tg@shelx.uni-ac.gwdg.de Overview The Reciprocal Lattice The
More informationCRYSTALLOGRAPHY AND STORYTELLING WITH DATA. President, Association of Women in Science, Bethesda Chapter STEM Consultant
CRYSTALLOGRAPHY AND STORYTELLING WITH DATA President, Association of Women in Science, Bethesda Chapter STEM Consultant MY STORY Passion for Science BS Biology Major MS Biotechnology & Project in Bioinformatics
More informationScattering by two Electrons
Scattering by two Electrons p = -r k in k in p r e 2 q k in /λ θ θ k out /λ S q = r k out p + q = r (k out - k in ) e 1 Phase difference of wave 2 with respect to wave 1: 2π λ (k out - k in ) r= 2π S r
More informationCrystallographic Point Groups and Space Groups
Crystallographic Point Groups and Space Groups Physics 251 Spring 2011 Matt Wittmann University of California Santa Cruz June 8, 2011 Mathematical description of a crystal Definition A Bravais lattice
More informationTables of crystallographic properties of double antisymmetry space groups
Tables of crystallographic properties of double antisymmetry space groups Mantao Huang a, Brian K. VanLeeuwen a, Daniel B. Litvin b and Venkatraman Gopalan a * a Department of Materials Science and Engineering,
More informationDrug targets, Protein Structures and Crystallography
Drug targets, Protein Structures and Crystallography NS5B viral RNA polymerase (RNA dep) Hepa88s C drug Sofosbuvir (Sovaldi) FDA 2013 Epclusa - combina8on with Velpatasvir approved in in 2016) Prodrug
More informationSPACE GROUPS AND SYMMETRY
SPACE GROUPS AND SYMMETRY Michael Landsberg Electron Crystallography Workshop C-CINA, Basel, 1-7 Aug 2010 m.landsberg@uq.edu.au Averaging Why single molecule EM techniques are far superior in resolution
More informationChapter 4. Crystallography. 4.1 The crystalline state
Crystallography Atoms form bonds which attract them to one another. When you put many atoms together and they form bonds amongst themselves, are there any rules as to how they order themselves? Can we
More informationRoad map (Where are we headed?)
Road map (Where are we headed?) oal: Fairly high level understanding of carrier transport and optical transitions in semiconductors Necessary Ingredients Crystal Structure Lattice Vibrations Free Electron
More informationDiffraction. X-ray diffraction
Diffraction Definition (from Cambridge Advanced Learner s Dictionary ): - diffraction noun [U] SPECIALIZED (a pattern caused by) a change in the direction of light, water or sound waves - diffract verb
More information6. X-ray Crystallography and Fourier Series
6. X-ray Crystallography and Fourier Series Most of the information that we have on protein structure comes from x-ray crystallography. The basic steps in finding a protein structure using this method
More informationWave diffraction and the reciprocal lattice
Wave diffraction and the reciprocal lattice Dept of Phys M.C. Chang Braggs theory of diffraction Reciprocal lattice von Laue s theory of diffraction Braggs view of the diffraction (1912, father and son)
More informationThe Solid State. Phase diagrams Crystals and symmetry Unit cells and packing Types of solid
The Solid State Phase diagrams Crystals and symmetry Unit cells and packing Types of solid Learning objectives Apply phase diagrams to prediction of phase behaviour Describe distinguishing features of
More informationChapter 2. X-ray X. Diffraction and Reciprocal Lattice. Scattering from Lattices
Chapter. X-ray X Diffraction and Reciprocal Lattice Diffraction of waves by crystals Reciprocal Lattice Diffraction of X-rays Powder diffraction Single crystal X-ray diffraction Scattering from Lattices
More informationSurface Sensitivity & Surface Specificity
Surface Sensitivity & Surface Specificity The problems of sensitivity and detection limits are common to all forms of spectroscopy. In its simplest form, the question of sensitivity boils down to whether
More informationIntroduction to. Crystallography
M. MORALES Introuction to Crystallography magali.morales@ensicaen.fr Classification of the matter in 3 states : Crystallise soli liqui or amorphous gaz soli Crystallise soli : unique arrangement of atoms
More informationDetermining Protein Structure BIBC 100
Determining Protein Structure BIBC 100 Determining Protein Structure X-Ray Diffraction Interactions of x-rays with electrons in molecules in a crystal NMR- Nuclear Magnetic Resonance Interactions of magnetic
More informationEarth Materials Lab 2 - Lattices and the Unit Cell
Earth Materials Lab 2 - Lattices and the Unit Cell Unit Cell Minerals are crystallographic solids and therefore are made of atoms arranged into lattices. The average size hand specimen is made of more
More informationLecture Note on Crystal structures Masatsugu Sei Suzuki and Itsuko S. Suzuki Department of Physics, SUNY at Binghamton (Date: February 03, 2012)
Lecture Note on Crystal structures Masatsugu Sei Suzuki and Itsuko S. Suzuki Department of Physics, SUNY at Binghamton (Date: February 03, 2012) This is a part of lecture note on solid state physics (Phys.472/572)
More informationCRYSTAL STRUCTURE, PHASE CHANGES, AND PHASE DIAGRAMS
CRYSTAL STRUCTURE, PHASE CHANGES, AND PHASE DIAGRAMS CRYSTAL STRUCTURE CRYSTALLINE AND AMORPHOUS SOLIDS Crystalline solids have an ordered arrangement. The long range order comes about from an underlying
More informationPSD '18 -- Xray lecture 4. Laue conditions Fourier Transform The reciprocal lattice data collection
PSD '18 -- Xray lecture 4 Laue conditions Fourier Transform The reciprocal lattice data collection 1 Fourier Transform The Fourier Transform is a conversion of one space into another space with reciprocal
More informationLattices and Symmetry Scattering and Diffraction (Physics)
Lattices and Symmetry Scattering and Diffraction (Physics) James A. Kaduk INEOS Technologies Analytical Science Research Services Naperville IL 60566 James.Kaduk@innovene.com 1 Harry Potter and the Sorcerer
More informationHow to study minerals?!
How to study minerals?! ü What tools did scientists have from pre-history to Renaissance? Eyes and measuring devices Calcite Crystal faces! ü One of the most spectacular aspect of minerals ü NOTE: No mention
More informationTim Hughbanks CHEMISTRY 634. Two Covers. Required Books, etc.
CHEMISTRY 634 This course is for 3 credits. Lecture: 2 75 min/week; TTh 11:10-12:25, Room 2122 Grades will be based on the homework (roughly 25%), term paper (15%), midterm and final exams Web site: http://www.chem.tamu.edu/rgroup/
More informationA web based crystallographic tool for the construction of nanoparticles
A web based crystallographic tool for the construction of nanoparticles Alexios Chatzigoulas 16/5/2018 + = 1 Outline Introduction Motivation Crystallography theory Creation of a web based crystallographic
More informationCRYSTALLOGRAPHIC POINT AND SPACE GROUPS. Andy Elvin June 10, 2013
CRYSTALLOGRAPHIC POINT AND SPACE GROUPS Andy Elvin June 10, 2013 Contents Point and Space Groups Wallpaper Groups X-Ray Diffraction Electron Wavefunction Neumann s Principle Magnetic Point Groups Point
More informationChapter 2 Introduction to Phenomenological Crystal Structure
Chapter 2 Introduction to Phenomenological Crystal Structure 2.1 Crystal Structure An ideal crystal represents a periodic pattern generated by infinite, regular repetition of identical microphysical structural
More informationFundamentals. Crystal patterns and crystal structures. Lattices, their symmetry and related basic concepts
Fundamentals. Crystal patterns and crystal structures. Lattices, their symmetry and related basic concepts Didactic material for the MaThCryst schools, France massimo.nespolo@univ-lorraine.fr Ideal vs.
More information1 Crystal Structures. of three-dimensional crystals. Here we use two-dimensional examples to illustrate the concepts.
3 1 Crystal Structures A crystal is a periodic array of atoms. Many elements and quite a few compounds are crystalline at low enough temperatures, and many of the solid materials in our everyday life (like
More informationSolids. properties & structure
Solids properties & structure Determining Crystal Structure crystalline solids have a very regular geometric arrangement of their particles the arrangement of the particles and distances between them is
More informationExperiment 3: Simulating X-Ray Diffraction CH3500: Inorganic Chemistry, Plymouth State University
Experiment 3: Simulating X-Ray Diffraction CH3500: Inorganic Chemistry, Plymouth State University Created by Jeremiah Duncan, Dept. of Atmospheric Science and Chemistry, Plymouth State University (2012).
More informationCrystal Structure and Electron Diffraction
Crystal Structure and Electron Diffraction References: Kittel C.: Introduction to Solid State Physics, 8 th ed. Wiley 005 University of Michigan, PHY441-44 (Advanced Physics Laboratory Experiments, Electron
More information