X-ray Crystallography
|
|
- Matilda Hudson
- 6 years ago
- Views:
Transcription
1 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 1896 X-rays from Wilhelm von Röntgen 1913 Bragg first small molecule 1950's or early 60's first proteins (myoglobin)
2 Andrew Torda 2009/11/25 [ 2 ] Where to learn best book "Crystallography made crystal clear", Rhodes, G, Academic press lectures Prof Betzel? Hamburg full of crystallographers
3 Andrew Torda 2009/11/25 [ 3 ] Steps From protein crystal crystal in front of X-ray source diffraction pattern (structure factors) structure factors coordinates fourier tranform + phasing coordinates better coordinates
4 2009/11/25 [ 4 ] Proteins and crystals Proteins can form crystals like table salt or sugar just much more difficult a, b, c define the unit cell may not be perpendicular may contain several copies usually - protein + water + salt sometimes ligand b a
5 2009/11/25 [ 5 ] Making crystals do you normally see protein crystals? what scale? << mm usually rather difficult concentrated, rather pure protein put in a drop, concentrate more by diffusion / evaporation repeat many times with different conditions buffer, solvent, ph, temperature partially automated (expensive) rather empirical
6 photo from Manfred Weiss Andrew Torda 2009/11/25 [ 6 ] 1mm
7 diagram from www-structmed.cimr.cam.ac.uk/course/overview/overview.html Andrew Torda 2009/11/25 [ 7 ] The measurement x-ray source detector CCD detector (/ film) from this data to a set of coordinates
8 Andrew Torda 2009/11/25 [ 8 ] Some necessary terms ρ is electron density ρ x,y,z where the atoms are F h,k,l 's are what comes from x-rays + proteins they have a phase one records an amplitude without phase h, k, l are indexes in the recorded data
9 2009/11/25 [ 9 ] Proteins and X-rays light wavelength x 10-9 m (about 4000 bonds) x-rays have wavelengths near 1 Å (10-10 m) no such thing as X-ray lens cannot focus, cannot record an image x-rays are diffracted by electron clouds H atoms hardly any electrons (almost invisible) C, N, O (+ P, S,..) do diffract heavy atoms less biological diffract most (Hg, Se)
10 Andrew Torda 2009/11/25 [ 10 ] From protein to diffraction Start with reverse problem shine light on two holes important for pattern r AB λ (wavelength)
11 Andrew Torda 2009/11/25 [ 11 ] Diffraction by a grid pattern on this side is regular r AB, λ (wavelength)
12 Andrew Torda 2009/11/25 [ 12 ] One and more waves What does one wave look like? 2π y ( x ) = A cos x + α λ For some amplitude A, phase shift α often neglect wavelength λ wavelengths are the same If one adds some waves together
13 Andrew Torda 2009/11/25 [ 13 ] amplitude Adding waves (same frequency) same frequency diff amplitudes x amplitude sum one wave same frequency different amplitude x amplitude of this wave? will depend on phases
14 Andrew Torda 2009/11/25 [ 14 ] What one records lots of scatterering atoms / electron clouds lots of waves b amplitude x each one of these waves is a sum of others has a contribution from all atoms a
15 Andrew Torda 2009/11/25 [ 15 ] From protein to diffraction If we know the protein coordinates x-ray source detector One should be able to calculate the pattern scattering from one site one dimension 2π y ( x ) = A cos x + α λ
16 Andrew Torda 2009/11/25 [ 16 ] earlier formalise the relation 2π y ( x ) = A cos x + α λ here wavelength (λ) is the same 2πihx change nomenclature f = e phase information is hiding in 2πhx 2 i( hx+ ky+ lz) go to three dimensions f = e π sum over lots of waves n = scatterers F hkl e j= 1 2πi ( hx + ky + lz ) j j j phase information is hiding in hkl
17 Andrew Torda 2009/11/25 [ 17 ] From protein to diffraction x-ray source detector F is the structure factor n indexed by hkl F hkl = e j= 1 summation runs over all scatterers electron clouds periodic functions each scatterer contributes to all reflections 2πi ( hx + ky + lz ) j j j
18 Andrew Torda 2009/11/25 [ 18 ] before What is recorded no phases F hkl = n j= 1 e 2πi ( hx + ky + lz ) j j j make the volume explicit put in the electron density ρ Fhkl F has phase not recorded really F 2 is recorded (no phase) = V ρ x, y, z e 2πi ( hx+ ky+ lz ) dv we want ρ x,y,z if we know the phases can reverse Fourier transform ρ x, y, z = V 1 h k l F h, k, l e 2πi ( hx+ ky+ lz )
19 Andrew Torda 2009/11/25 [ 19 ] From scattering to coordinates from coordinates to data (no phases) F hkl = V ρ x, y, z e 2πi ( hx+ ky+ lz ) dv from data to coordinates if you knew the phases of F h,k,l 's each reflection contains contribution from all atoms each atom Stop here make points clear ρ x, y, z = V 1 h k l F h, k, l e 2πi ( hx+ ky+ lz )
20 Andrew Torda 2009/11/25 [ 20 ] Summary so far Given the coordinates for atoms in a crystal can calculate the expected reflections (used later) want the electron density ρ x,y,z (atomic coordinates) fourier transform of reflections with phases from somewhere else each reflection depends on all atoms (ρ x,y,z ) electron density ρ x,y,z depends on all observed reflections
21 Andrew Torda 2009/11/25 [ 21 ] Summary so far most things are additive add more scatterers, add more components to F F hkl is somewhat abstract an amplitude with a phase the phase is not measured if one does know the phase one can get F hkl
22 Andrew Torda 2009/11/25 [ 22 ] How to get phases two methods dominate MR (molecular replacement) about 80 % of structures MIR (multiple isomorphous replacement) MIR
23 Andrew Torda 2009/11/25 [ 23 ] MIR structure with two or three atoms (not 1000's) one could record data get the phases by brute force (direct) what if one has some huge atoms in a protein? they would affect all the reflections one could still get their phases directly heavy atoms
24 Andrew Torda 2009/11/25 [ 24 ] MIR Record data from protein (F P ) Record data from protein + heavy atoms (F PH ) get difference (F PH -F P ) call this F H use this for coordinates and phases of heavy atoms call these phases α H go back to (F PH ) get phases of original data you know the positions of heavy atoms For each original reflection F P = F PH F H now have phased reflections for protein back Fourier transform to get ρ
25 Andrew Torda 2009/11/25 [ 25 ] MIR some details and formalism skipped really need more than one heavy atom type ambiguities chemistry what are heavy atoms? something with lots of electrons should bind at specific positions to protein
26 Andrew Torda 2009/11/25 [ 26 ] MIR examples Selenomethionine replaces methionine very little change to protein about 5000 examples in PDB very specific positions in protein special molecular biology techniques used put in a solution with heavy metal salt fast, cheap put in solution with large anion Br, I put under pressure with noble gas Xe, Kr
27 Andrew Torda 2009/11/25 [ 27 ] MIR problems chemical problems not always easy fundamental problems protein, protein + heavy atoms not identical maths assumes that F PH = F P + F H initial phases should be good, but not perfect refinement necessary (later)
28 Andrew Torda 2009/11/25 [ 28 ] phasing by MR / molecular replacement Problem you have crystals recorded reflections want phases to calculate ρ x,y,z what one needs for MR structure of similar molecule
29 Andrew Torda 2009/11/25 [ 29 ] MR (simplified) if we know related structure can calculate F with phases can calculate amplitudes (observed data) calculated calculated
30 Andrew Torda 2009/11/25 [ 30 ] MR use a simplified function to get rotations and translations call these correction factors we have F model F protein = F model corrections problems model is not identical to protein of interest 90 % sequence identity, similar length no problem 10 % sequence identity, different sizes will not work the initial phases may be roughly right but not perfect remember this was the case with MIR - refinement
31 Andrew Torda 2009/11/25 [ 31 ] more phasing / refinement whatever method we have initial phases calculate F hkl inverse fourier transform yields electron density not finished density is not very accurate (poor phases) try to adjust phases so as to get sharpest electron density
32 Andrew Torda 2009/11/25 [ 32 ] more refinement one has electron density ρ the atoms have to be fit into it electron density is not perfect where the atoms go is not simple atoms are mobile high mobility B factor higher we can calculate electron density from coordinates variables (at least) x, y, z, B
33 Andrew Torda 2009/11/25 [ 33 ] more refinement model / coordinates calculate density ρ adjust coordinates of atoms maybe adjust B factors calculate F hkl gives F calc to adjust, compare F calc and F obs calculated from model, observed measured
34 Andrew Torda 2009/11/25 [ 34 ] Refinement from my model I can calculate F from F I can calculate the amplitude I would measure call this F calc from my measurements I have F obs if model and phases are perfect each F calc = F obs refinement adjust coordinates of atoms in model adjust phases minimise F calc F obs I have many F 's my function summed over all reflections
35 Andrew Torda 2009/11/25 [ 35 ] R factor what I care about is j h, k, l calc F j F obs j normalise and use standard definition R = 100 j h, k, l F calc j j h, k, l F obs j F obs j slightly change recipe for refinement
36 Andrew Torda 2009/11/25 [ 36 ] model / coordinates calculate density ρ adjust coordinates of atoms maybe adjust B factors calculate F hkl gives F calc calculate R factor
37 Andrew Torda 2009/11/25 [ 37 ] R factor most structures are % F j h, k, l R = 100 is this enough? j what if there is over fitting? how to test? common form of cross validation take maybe 10 % of data and remove refine on 90 % of data calculate R based on the 10 % not used called R free calc j h, k, l F obs j F obs j
38 Andrew Torda 2009/11/25 [ 38 ] Resolution nλ = = length ABC 2d sinθ nλ d = 2sinθ A 2θ B C d d is the smallest distance one can resolve wavelength λ - smaller better angle θ can one adjust θ? not really...
39 Andrew Torda 2009/11/25 [ 39 ] diffraction angle / resolution high resolution few Å x-ray source low resolution different picture
40 Andrew Torda 2009/11/25 [ 40 ] diffraction and resolution the higher resolution spots are harder to see
41 Andrew Torda 2009/11/25 [ 41 ] Different resolution - effects Movie time - ucxray.berkeley.edu/~jamesh/movies/ At <1.0 Å see atoms at 5 Å tryptophans disappear typical for big and difficult structures
42 Andrew Torda 2009/11/25 [ 42 ] diffraction and resolution typical resolution in PDB 1.5 to 2.5 Å resolution could you just record longer? molecule would be toasted middle would be black how far can you go? limits for each protein
43 Andrew Torda 2009/11/25 [ 43 ] Atomic motion what if the atoms move by 2 Å? can never really define the coordinates of the atom typical of loops and termini
44 Andrew Torda 2009/11/25 [ 44 ] Static disorder perfect crystal imperfect crystal In each copy of the molecule atoms are in different place coordinates of atoms are not defined to 1, 2,.. Å you cannot collect high resolution data
45 Andrew Torda 2009/11/25 [ 45 ] disorder static versus dynamic not easy to distinguish model for atomic motion? gaussian real meaning of B factor width of Gaussian density = ( x µ ) σ 2 2πσ e density space
46 Andrew Torda 2009/11/25 [ 46 ] Back to PDB files x, y, z coordinates B factors sometimes for each atom for each residue at top of file R factor, R free optional information about conditions, phasing amount of data (1000's of reflections) software used for refinement still some errors.. example
47 2009/11/25 [ 47 ] how difficult is fitting density? errors can be made backwards wrong sequence cannot tell O from N
48 Andrew Torda 2009/11/25 [ 48 ] Summarise and compare with NMR overall procedure crystallise collect data phase refine (x, y, z, B) check R
49 Andrew Torda 2009/11/25 [ 49 ] NMR and X-ray NMR X-ray resolution model how different are the solutions formally a Gaussian resolution not well defined 1.5 to 2.5 Å size many examples >10 3 residues few examples > 200 residues
Protein crystallography. Garry Taylor
Protein crystallography Garry Taylor X-ray Crystallography - the Basics Grow crystals Collect X-ray data Determine phases Calculate ρ-map Interpret map Refine coordinates Do the biology. Nitrogen at -180
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 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 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 informationWhat is the Phase Problem? Overview of the Phase Problem. Phases. 201 Phases. Diffraction vector for a Bragg spot. In General for Any Atom (x, y, z)
Protein Overview of the Phase Problem Crystal Data Phases Structure John Rose ACA Summer School 2006 Reorganized by Andy Howard,, Spring 2008 Remember We can measure reflection intensities We can calculate
More informationCrystal lattice Real Space. Reflections Reciprocal Space. I. Solving Phases II. Model Building for CHEM 645. Purified Protein. Build model.
I. Solving Phases II. Model Building for CHEM 645 Purified Protein Solve Phase Build model and refine Crystal lattice Real Space Reflections Reciprocal Space ρ (x, y, z) pronounced rho F hkl 2 I F (h,
More informationPhase problem: Determining an initial phase angle α hkl for each recorded reflection. 1 ρ(x,y,z) = F hkl cos 2π (hx+ky+ lz - α hkl ) V h k l
Phase problem: Determining an initial phase angle α hkl for each recorded reflection 1 ρ(x,y,z) = F hkl cos 2π (hx+ky+ lz - α hkl ) V h k l Methods: Heavy atom methods (isomorphous replacement Hg, Pt)
More informationElectron Density at various resolutions, and fitting a model as accurately as possible.
Section 9, Electron Density Maps 900 Electron Density at various resolutions, and fitting a model as accurately as possible. ρ xyz = (Vol) -1 h k l m hkl F hkl e iφ hkl e-i2π( hx + ky + lz ) Amplitude
More informationCS273: Algorithms for Structure Handout # 13 and Motion in Biology Stanford University Tuesday, 11 May 2003
CS273: Algorithms for Structure Handout # 13 and Motion in Biology Stanford University Tuesday, 11 May 2003 Lecture #13: 11 May 2004 Topics: Protein Structure Determination Scribe: Minli Zhu We acknowledge
More informationProtein Structure Determination 9/25/2007
One-dimensional NMR spectra Ethanol Cellulase (36 a.a.) Branden & Tooze, Fig. 18.16 1D and 2D NMR spectra of inhibitor K (57 a.a.) K. Wuthrich, NMR of Proteins and Nucleic Acids. (Wiley, 1986.) p. 54-55.
More informationSummary of Experimental Protein Structure Determination. Key Elements
Programme 8.00-8.20 Summary of last week s lecture and quiz 8.20-9.00 Structure validation 9.00-9.15 Break 9.15-11.00 Exercise: Structure validation tutorial 11.00-11.10 Break 11.10-11.40 Summary & discussion
More informationAnomalous dispersion
Selenomethionine MAD Selenomethionine is the amino acid methionine with the Sulfur replaced by a Selenium. Selenium is a heavy atom that also has the propery of "anomalous scatter" at some wavelengths,
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 informationStructure factors again
Structure factors again Remember 1D, structure factor for order h F h = F h exp[iα h ] = I 01 ρ(x)exp[2πihx]dx Where x is fractional position along unit cell distance (repeating distance, origin arbitrary)
More informationSOLID STATE 9. Determination of Crystal Structures
SOLID STATE 9 Determination of Crystal Structures In the diffraction experiment, we measure intensities as a function of d hkl. Intensities are the sum of the x-rays scattered by all the atoms in a crystal.
More informationDirect Method. Very few protein diffraction data meet the 2nd condition
Direct Method Two conditions: -atoms in the structure are equal-weighted -resolution of data are higher than the distance between the atoms in the structure Very few protein diffraction data meet the 2nd
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 informationMacromolecular X-ray Crystallography
Protein Structural Models for CHEM 641 Fall 07 Brian Bahnson Department of Chemistry & Biochemistry University of Delaware Macromolecular X-ray Crystallography Purified Protein X-ray Diffraction Data collection
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 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 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 informationSHELXC/D/E. Andrea Thorn
SHELXC/D/E Andrea Thorn What is experimental phasing? Experimental phasing is what you do if MR doesn t work. What is experimental phasing? Experimental phasing methods depend on intensity differences.
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 informationCCP4 Diamond 2014 SHELXC/D/E. Andrea Thorn
CCP4 Diamond 2014 SHELXC/D/E Andrea Thorn SHELXC/D/E workflow SHELXC: α calculation, file preparation SHELXD: Marker atom search = substructure search SHELXE: density modification Maps and coordinate files
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 informationMaterials 286C/UCSB: Class VI Structure factors (continued), the phase problem, Patterson techniques and direct methods
Materials 286C/UCSB: Class VI Structure factors (continued), the phase problem, Patterson techniques and direct methods Ram Seshadri (seshadri@mrl.ucsb.edu) Structure factors The structure factor for a
More informationX- ray crystallography. CS/CME/Biophys/BMI 279 Nov. 12, 2015 Ron Dror
X- ray crystallography CS/CME/Biophys/BMI 279 Nov. 12, 2015 Ron Dror 1 Outline Overview of x-ray crystallography Crystals Electron density Diffraction patterns The computational problem: determining structure
More informationProtein structures and comparisons ndrew Torda Bioinformatik, Mai 2008
Protein structures and comparisons ndrew Torda 67.937 Bioinformatik, Mai 2008 Ultimate aim how to find out the most about a protein what you can get from sequence and structure information On the way..
More informationMolecular Biology Course 2006 Protein Crystallography Part II
Molecular Biology Course 2006 Protein Crystallography Part II Tim Grüne University of Göttingen Dept. of Structural Chemistry December 2006 http://shelx.uni-ac.gwdg.de tg@shelx.uni-ac.gwdg.de Overview
More informationBC530 Class notes on X-ray Crystallography
BC530 Class notes on X-ray Crystallography web material: Ethan A Merritt http://skuld.bmsc.washington.edu/~merritt/bc530/ October 11, 2016 Growing Crystals It should be self-evident that in order to do
More informationWhy do We Trust X-ray Crystallography?
Why do We Trust X-ray Crystallography? Andrew D Bond All chemists know that X-ray crystallography is the gold standard characterisation technique: an X-ray crystal structure provides definitive proof of
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 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 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 informationProtein Crystallography Part II
Molecular Biology Course 2007 Protein Crystallography Part II Tim Grüne University of Göttingen Dept. of Structural Chemistry November 2007 http://shelx.uni-ac.gwdg.de tg@shelx.uni-ac.gwdg.de Overview
More informationProteins. Central Dogma : DNA RNA protein Amino acid polymers - defined composition & order. Perform nearly all cellular functions Drug Targets
Proteins Central Dogma : DNA RNA protein Amino acid polymers - defined composition & order Perform nearly all cellular functions Drug Targets Fold into discrete shapes. Proteins - cont. Specific shapes
More informationMacromolecular Crystallography Part II
Molecular Biology Course 2009 Macromolecular Crystallography Part II Tim Grüne University of Göttingen Dept. of Structural Chemistry November 2009 http://shelx.uni-ac.gwdg.de tg@shelx.uni-ac.gwdg.de From
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 informationExperimental phasing, Pattersons and SHELX Andrea Thorn
Experimental phasing, Pattersons and SHELX Andrea Thorn What is experimental phasing? Experimental phasing is what you do if MR doesn t work. What is experimental phasing? Experimental phasing methods
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 informationStructure Factors F HKL. Fobs = k I HKL magnitude of F only from expt
Structure Factors F HKL Fobs = k I HKL magnitude of F only from expt F calc = Σ f i {cos(2π(hx i + ky i + lz i )) + i sin(2π(hx i + ky i + lz i ))} sum over all atom locations (x,y,z) where f i is the
More informationStructure Factors. How to get more than unit cell sizes from your diffraction data.
Structure Factors How to get more than unit cell sizes from your diffraction data http://homepages.utoledo.edu/clind/ Yet again expanding convenient concepts First concept introduced: Reflection from lattice
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 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 informationHandout 12 Structure refinement. Completing the structure and evaluating how good your data and model agree
Handout 1 Structure refinement Completing the structure and evaluating how good your data and model agree Why you should refine a structure We have considered how atoms are located by Patterson, direct
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 informationLikelihood and SAD phasing in Phaser. R J Read, Department of Haematology Cambridge Institute for Medical Research
Likelihood and SAD phasing in Phaser R J Read, Department of Haematology Cambridge Institute for Medical Research Concept of likelihood Likelihood with dice 4 6 8 10 Roll a seven. Which die?? p(4)=p(6)=0
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 informationScattering Lecture. February 24, 2014
Scattering Lecture February 24, 2014 Structure Determination by Scattering Waves of radiation scattered by different objects interfere to give rise to an observable pattern! The wavelength needs to close
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 informationPart 1 X-ray Crystallography
Part 1 X-ray Crystallography What happens to electron when it is hit by x-rays? 1. The electron starts vibrating with the same frequency as the x-ray beam 2. As a result, secondary beams will be scattered
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 informationTLS and all that. Ethan A Merritt. CCP4 Summer School 2011 (Argonne, IL) Abstract
TLS and all that Ethan A Merritt CCP4 Summer School 2011 (Argonne, IL) Abstract We can never know the position of every atom in a crystal structure perfectly. Each atom has an associated positional uncertainty.
More informationBiology III: Crystallographic phases
Haupt/Masterstudiengang Physik Methoden moderner Röntgenphysik II: Streuung und Abbildung SS 2013 Biology III: Crystallographic phases Thomas R. Schneider, EMBL Hamburg 25/6/2013 thomas.schneider@embl-hamburg.de
More informationRoger Johnson Structure and Dynamics: X-ray Diffraction Lecture 6
6.1. Summary In this Lecture we cover the theory of x-ray diffraction, which gives direct information about the atomic structure of crystals. In these experiments, the wavelength of the incident beam must
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 informationSummary: Crystallography in a nutshell. Lecture no. 4. (Crystallography without tears, part 2)
Structure Determination Summary: Crystallography in a nutshell. Lecture no. 4. (Crystallography without tears, part 2) Cele Abad-Zapatero University of Illinois at Chicago Center for Pharmaceutical Biotechnology.
More informationPymol Practial Guide
Pymol Practial Guide Pymol is a powerful visualizor very convenient to work with protein molecules. Its interface may seem complex at first, but you will see that with a little practice is simple and powerful
More information11/6/2013. Refinement. Fourier Methods. Fourier Methods. Difference Map. Difference Map Find H s. Difference Map No C 1
Refinement Fourier Methods find heavy atom or some F s phases using direct methods locate new atoms, improve phases continue until all atoms found in more or less correct position starting point of refinement
More informationX-ray Diffraction. Diffraction. X-ray Generation. X-ray Generation. X-ray Generation. X-ray Spectrum from Tube
X-ray Diffraction Mineral identification Mode analysis Structure Studies X-ray Generation X-ray tube (sealed) Pure metal target (Cu) Electrons remover inner-shell electrons from target. Other electrons
More informationIgE binds asymmetrically to its B cell receptor CD23
Supplementary Information IgE binds asymmetrically to its B cell receptor CD23 Balvinder Dhaliwal 1*, Marie O. Y. Pang 2, Anthony H. Keeble 2,3, Louisa K. James 2,4, Hannah J. Gould 2, James M. McDonnell
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 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 informationBiological Small Angle X-ray Scattering (SAXS) Dec 2, 2013
Biological Small Angle X-ray Scattering (SAXS) Dec 2, 2013 Structural Biology Shape Dynamic Light Scattering Electron Microscopy Small Angle X-ray Scattering Cryo-Electron Microscopy Wide Angle X- ray
More informationDetermination of the Substructure
Monday, June 15 th, 2009 Determination of the Substructure EMBO / MAX-INF2 Practical Course http://shelx.uni-ac.gwdg.de Overview Substructure Definition and Motivation Extracting Substructure Data from
More informationRietveld Structure Refinement of Protein Powder Diffraction Data using GSAS
Rietveld Structure Refinement of Protein Powder Diffraction Data using GSAS Jon Wright ESRF, Grenoble, France Plan This is a users perspective Cover the protein specific aspects (assuming knowledge of
More informationMolecular Replacement (Alexei Vagin s lecture)
Molecular Replacement (Alexei Vagin s lecture) Contents What is Molecular Replacement Functions in Molecular Replacement Weighting scheme Information from data and model Some special techniques of Molecular
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 informationX-ray Crystallography I. James Fraser Macromolecluar Interactions BP204
X-ray Crystallography I James Fraser Macromolecluar Interactions BP204 Key take-aways 1. X-ray crystallography results from an ensemble of Billions and Billions of molecules in the crystal 2. Models in
More informationMolecular Modeling lecture 2
Molecular Modeling 2018 -- lecture 2 Topics 1. Secondary structure 3. Sequence similarity and homology 2. Secondary structure prediction 4. Where do protein structures come from? X-ray crystallography
More informationGBS765 Electron microscopy
GBS765 Electron microscopy Lecture 1 Waves and Fourier transforms 10/14/14 9:05 AM Some fundamental concepts: Periodicity! If there is some a, for a function f(x), such that f(x) = f(x + na) then function
More informationData Collection. Overview. Methods. Counter Methods. Crystal Quality with -Scans
Data Collection Overview with a unit cell, possible space group and computer reference frame (orientation matrix); the location of diffracted x-rays can be calculated (h k l) and intercepted by something
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 informationX-ray crystallography
X-ray crystallography Sources: 1. The Elements of Physical Chemistry by Peter Atkins (including some nice color slides incorporated into these lectures) 2. Physical Chemistry by Tinoco, Sauer, Wang and
More informationIntroduction to" Protein Structure
Introduction to" Protein Structure Function, evolution & experimental methods Thomas Blicher, Center for Biological Sequence Analysis Learning Objectives Outline the basic levels of protein structure.
More informationImage definition evaluation functions for X-ray crystallography: A new perspective on the phase. problem. Hui LI*, Meng HE* and Ze ZHANG
Image definition evaluation functions for X-ray crystallography: A new perspective on the phase problem Hui LI*, Meng HE* and Ze ZHANG Beijing University of Technology, Beijing 100124, People s Republic
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 informationThere and back again A short trip to Fourier Space. Janet Vonck 23 April 2014
There and back again A short trip to Fourier Space Janet Vonck 23 April 2014 Where can I find a Fourier Transform? Fourier Transforms are ubiquitous in structural biology: X-ray diffraction Spectroscopy
More informationTwo Lectures in X-ray Crystallography
Biochemistry 503 Michael Wiener (mwiener@virginia.edu, 3-2731, Snyder 360) Two Lectures in X-ray Crystallography Outline 1. Justification & introductory remarks 2. Experimental setup 3. Protein crystals
More informationPROBING CRYSTAL STRUCTURE
PROBING CRYSTAL STRUCTURE Andrew Baczewski PHY 491, October 10th, 2011 OVERVIEW First - we ll briefly discuss Friday s quiz. Today, we will answer the following questions: How do we experimentally probe
More informationProtein Struktur (optional, flexible)
Protein Struktur (optional, flexible) 22/10/2009 [ 1 ] Andrew Torda, Wintersemester 2009 / 2010, AST nur für Informatiker, Mathematiker,.. 26 kt, 3 ov 2009 Proteins - who cares? 22/10/2009 [ 2 ] Most important
More informationKeble College - Hilary 2012 Section VI: Condensed matter physics Tutorial 2 - Lattices and scattering
Tomi Johnson Keble College - Hilary 2012 Section VI: Condensed matter physics Tutorial 2 - Lattices and scattering Please leave your work in the Clarendon laboratory s J pigeon hole by 5pm on Monday of
More informationNon-bonded interactions
speeding up the number-crunching Marcus Elstner and Tomáš Kubař May 8, 2015 why care? key to understand biomolecular structure and function binding of a ligand efficiency of a reaction color of a chromophore
More informationReaction Landscape of a Pentadentate N5-Ligated Mn II Complex with O 2
Electronic Supplementary Information for: Reaction Landscape of a Pentadentate N5-Ligated Mn II Complex with O - and H O Includes Conversion of a Peroxomanganese(III) Adduct to a Bis(µ- O)dimanganese(III,IV)
More informationInformation Content of EXAFS (I)
Content of EXAFS (I) Sometimes, we have beautiful data. This is the merge of 5 scans on a 50 nm film of GeSb on silica, at the Ge edge and measured in fluorescence at NSLS X23a2. Here, I show a Fourier
More informationSchematic representation of relation between disorder and scattering
Crystal lattice Reciprocal lattice FT Schematic representation of relation between disorder and scattering ρ = Δρ + Occupational disorder Diffuse scattering Bragg scattering ρ = Δρ + Positional
More informationStructural characterization. Part 1
Structural characterization Part 1 Experimental methods X-ray diffraction Electron diffraction Neutron diffraction Light diffraction EXAFS-Extended X- ray absorption fine structure XANES-X-ray absorption
More informationSmall-Angle X-ray Scattering (SAXS) SPring-8/JASRI Naoto Yagi
Small-Angle X-ray Scattering (SAXS) SPring-8/JASRI Naoto Yagi 1 Wikipedia Small-angle X-ray scattering (SAXS) is a small-angle scattering (SAS) technique where the elastic scattering of X-rays (wavelength
More informationGood Vibrations Studying phonons with momentum resolved spectroscopy. D.J. Voneshen 20/6/2018
Good Vibrations Studying phonons with momentum resolved spectroscopy D.J. Voneshen 20/6/2018 Overview What probe to use? Types of instruments. Single crystals example Powder example Thing I didn t talk
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 informationde Broglie Waves h p de Broglie argued Light exhibits both wave and particle properties
de Broglie argued de Broglie Waves Light exhibits both wave and particle properties Wave interference, diffraction Particle photoelectric effect, Compton effect Then matter (particles) should exhibit both
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 informationModule 03 Lecture 14 Inferential Statistics ANOVA and TOI
Introduction of Data Analytics Prof. Nandan Sudarsanam and Prof. B Ravindran Department of Management Studies and Department of Computer Science and Engineering Indian Institute of Technology, Madras Module
More informationPatterson Methods
59-553 Patterson Methods 113 In 1935, Patterson showed that the unknown phase information in the equation for electron density: ρ(xyz) = 1/V h k l F(hkl) exp[iα(hkl)] exp[-2πi(h x + k y + l z)] can be
More informationTwinning. Andrea Thorn
Twinning Andrea Thorn OVERVIEW Introduction: Definitions, origins of twinning Merohedral twins: Recognition, statistical analysis: H plot, Yeates Padilla plot Example Refinement and R values Reticular
More informationID14-EH3. Adam Round
Bio-SAXS @ ID14-EH3 Adam Round Contents What can be obtained from Bio-SAXS Measurable parameters Modelling strategies How to collect data at Bio-SAXS Procedure Data collection tests Data Verification and
More informationThis semester. Books
Models mostly proteins from detailed to more abstract models Some simulation methods This semester Books None necessary for my group and Prof Rarey Molecular Modelling: Principles and Applications Leach,
More informationElectron Rutherford Backscattering, a versatile tool for the study of thin films
Electron Rutherford Backscattering, a versatile tool for the study of thin films Maarten Vos Research School of Physics and Engineering Australian National University Canberra Australia Acknowledgements:
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 information