Linking data and model quality in macromolecular crystallography. Kay Diederichs
|
|
- Samuel Fox
- 5 years ago
- Views:
Transcription
1 Linking data and model quality in macromolecular crystallography Kay Diederichs
2 Crystallography is highly successful Can we do better?
3 Error in experimental data Error = random + systematic Multiplicity of n reduces the Random = counting + detector random error by n Systematic = Radiation damage + absorption + nonmultiplicity does not necessarily linearities + vibrations + reduce the systematic error! instabilities + If you don t have good data, then you have no data at all. -Sung-Hou Kim If you don t have good data, then you must learn statistics. - James Holton
4 Crystallographic statistics - which indicators are being used? Data R-values: Rpim < Rmerge=Rsym < Rmeas n n 1 /n 1 I i ( hkl ) I ( hkl ) R pim= hkl i= 1 n I i ( hkl ) hkl i= 1 I i ( hkl ) I ( hkl ) R merge = hkl i= 1 n R meas = I i ( hkl ) hkl n n I ( hkl ) I ( hkl ) n 1 i= 1 i n I i (hkl ) hkl i=1 hkl i= 1 Model R-values: Rwork/Rfree F obs (hkl ) F calc (hkl ) R work / free= hkl F obs (hkl ) hkl I/σ (for unmerged or merged data!)
5 In search for a proxy
6 Decisions and compromises Which high-resolution cutoff for refinement? Higher resolution means better accuracy and maps But: high resolution yields high Rwork/Rfree! Basic questions: what to optimize? Is the data/model R-value a good predictor/indicator of model quality? How good need the data be; to what extent do the data influence the refinement result? What to refine, and when to stop? Overfitting? Which datasets/frames to include into scaling? Optimize consistency (Rmeas) or quality of merged data (Rpim, <I/σ>)? Systematic differences/errors? Completeness versus radiation damage? Anomalous signal (CCano)? Reject negative observations or unique reflections? The reason why this is difficult to answer R-value questions is that no proper mathematical theory exists that uses absolute differences; concerning the use of R-values, Crystallography is disconnected from mainstream Statistics
7 Conflicting views An appropriate choice of resolution cutoff is difficult and sometimes seems to be performed mainly to satisfy referees... Ideally, we would determine the point at which adding the next shell of data is not adding any statistically significant information... Rmerge is not a very useful criterion. P. Evans (2011) An introduction to data reduction: space-group determination, scaling and intensity statistics. Acta Cryst. D67, 282 "At the highest resolution shell, the Rmerge can be allowed to reach 30 40% for low-symmetry crystals and up to 60% for high-symmetry crystals, since in the latter case the redundancy is usually higher." A. Wlodawer, W. Minor, Z. Dauter and M. Jaskolski (2008) Protein crystallography for non-crystallographers, or how to get the best (but not more) from published macromolecular structures. FEBS J. 275, 1
8 2010 PDB depositions
9 The asymptotic behaviour of model and data R-values is different at high resolution Data R-values (Rpim, Rmerge, Rmeas): with resolution, go to infinity since the numerator is constant (determined by background), and the denominator approaches zero Model R-values (Rwork/free): the ratio of numerator and denominator approaches a constant for a random or wrong model (Wilson 1950) This means that at high resolution, a quantitative relation cannot exist between model and data R-values!
10 Crystallographic reasoning 1. Better data allow to obtain a better model 2. A better model has a lower Rfree, and a lower Rfree-Rwork gap 3. Comparison of model R-values is only meaningful when using the same data 4. Taken together, this leads to the paired refinement technique : compare models in terms of their R-values against the same data.
11 Example: Cysteine DiOxygenase (CDO; PDB 3ELN) re-refined against 15-fold weaker data Rmerge Rpim Rfree Rwork I/sigma
12 Is there information beyond the conservative hi-res cutoff? Paired refinement technique : refine at (e.g.) 2.0Å and at 1.9Å using the same starting model and refinement parameters since it is meaningless to compare R-values at different resolutions, calculate the overall R-values of the 1.9Å model at 2.0Å (main.number_of_macro_cycles=1 strategy=none fix_rotamers=false ordered_solvent=false) ΔR=R1.9(2.0)-R2.0(2.0)
13 Do the maps really get better? cooperation with JCSG: Henry van den Bedem, Ashley M. Deacon, Abhinav Kumar identified 5 structures where re-processing of existing raw data permits to extend the resolution by another Å, with full completeness reprocessing with XDS/MOSFLM; refinement with refmac/phenix.refine calculate real-space CC of map and model, using EDSTATS (CCP4) or phenix.resolve
14 Example 1/5
15 Summary I Rmerge should no longer be considered as useful for deciding on a high-resolution cutoff The paired refinement technique can prove that data should be used to higher resolution than a (Rmerge-based) conservative cutoff suggests
16 In search for a proxy
17 measuring data quality with a correlation coefficient Correlation coefficient has clear meaning and well-known statistical properties Significance of its value can be assessed by Student's t-test (e.g. CC>0.3 is significant at p=0.01 for n>100; CC>0.08 is significant at p=0.01 for n>1000) Apply this idea to crystallographic intensity data: use random half-datasets CC1/2 (called CC_Imean by SCALA/aimless, now CC1/2 ) From CC1/2, we can analytically estimate CC of the full dataset against the true (usually unmeasurable) intensities using 2 CC 1/ 2 CC*= 1+CC 1/2 (Karplus and Diederichs (2012) Science 336, 1030)
18 Data CCs CC1/2 CC* Δ I/sigma
19 What is a suitable resolution cutoff when using CC1/2? Results from Student's t-test tell statistical significance (p=0.001 marked w/ * in CORRECT.LP/XSCALE.LP) Data are usually insignificant if CC1/2 < 0.15 It depends on refinement program if it can make good use of weak data; in practice a bit higher cutoff is best (remember, for CCanom a value of 0.3 proved useful) Operational definition: resolution should be cut such that the best model results use paired refinement!
20 Model CCs We can define CCwork, CCfree as CCs calculated on Fcalc2 of the working and free set, against the experimental data CCwork and CCfree can be directly compared with CC* CC* Dashes: CCwork, CCfree against weak exp tl data Dots: CC work, CC free against strong 3ELN data
21 Quantitative relation between data and model CCs Refinement should make CCwork converge towards CC* (from lower values) Inadequate model, or systematic errors in data processing: CCwork remains < CC* If CCwork > CC*: the model is closer to the data, than the truth is to the data : overfitting Error Exp l data True data l e d o m First Distance to truth
22 Summary II CC1/2 assesses the statistical significance of data 2 CC 1/ 2 CC*= 1+CC 1/2 predicts the agreement of experimental data and true data; CC* is the upper limit for the CCwork /CCfree model quality indicators CC1/2, CC*, CCwork/CCfree table can be obtained from Phenix distribution; the routine is called phenix.cc_star
23 Four new concepts for improving crystallographic procedures Image courtesy of P.A. Karplus
24 Further uses of the paired refinement technique
25 Does merging with weak data improve the resulting data? dataset name CDO3 CDO4 CDO5 CDO3+4 CDO3+5 CDO4+5 CDO3+4+5 # observations (10837) (2389) (10838) (13657) (21717) (13655) (24518) # unique reflections (2008) (1316) (1982) (2013) (2013) (1995) (2013) completeness [%] 99.9 (98.7) 93.8 (79.3) 95.7 (98.0) 99.9 (98.8) 99.9 (98.8) 95.7 (98.0) 99.9 (98.8) Rmeas [%] 10.2 (294.0) 23.1 (431.1) 26.0 (395.6) 15.0 (314.7) 15.9 (332.6) 26.0 (401.4) 15.9 (339.8) <I/σ> (0.64) (0.21) 9.88 (0.19) (0.69) (0.87) (0.49) (0.91) CC1/2 in highest shell; # of pairs ; ; ; ; ; ; ; 2008 CC* in highest shell
26 Refinement: which data give the best model? dataset name CDO3 CDO4 CDO5 CDO3+4 CDO3+5 CDO4+5 CDO3+4+5 model CDO3 0,1855, CDO , CDO , CDO , CDO , CDO4+5 CDO , , , , , , , , , , , , ,
27 Summary III Data R-values of merged data do not in any useful way predict the refinement outcome CC and CC* do 1/2
28 Does removal of negative reflections improve the data? All data Only positive observations Only positive unique reflections
29 Why reject negative observations or unique reflections? Negative observations/unique reflections increase the data R-value Assuming that data R-values are a predictor of data quality, rejecting them should improve model quality Make the data look better to reviewers
30 Does removal of negative reflections improve the model? Results from paired refinement R-value against Refinement against All reflections Only positive unique reflections Only positive observations All reflections , , , Only positive unique , , , Only positive observations , , ,
31 Summary IV Throwing away negative observations / unique reflections beautifies the data R-values and <I/σ>, but lowers CC1/2 and produces worse models as shown by the paired refinement technique!
32 Acknowledgement Andy Karplus, Oregon State University (Corvallis, OR) References P.A. Karplus and K. Diederichs (2012) Linking Crystallographic Data with Model Quality. Science 336, K. Diederichs and P.A. Karplus (2013) Better models by discarding data? Acta Cryst D, in the press see also: P.R. Evans (2012) Resolving Some Old Problems in Protein Crystallography. Science 336,
33 Thank you! If you would like to obtain a PDF of the slides, send to kay.diederichs@uni-konstanz.de
34 Checking your imagination! Which data are better? Rmerge=80%, multiplicity=4 or Rmerge=100%, multiplicity=8? Model A is refined at 2.0 Å, Rwork/Rfree=18.0/22%, model B at 2.2 Å, Rwork/Rfree=16.0/20.5%. a) Which model is better? b) If you don't know the answer: which procedure to decide? Can one compare R-values that do not refer to the same sets of reflections? Can one estimate model error by formulas that disregard experimental errors (sigmas)? Can a model give Fcalc2 that are closer to the true Fcalc2 than the Iobs are against which it was refined? Why is there a gap between CC* and CCwork at low res (only)?
35 General references Data-collection strategies Z. Dauter (1999) Acta Cryst. D55, Integration of macromolecular diffraction data A.G.W. Leslie (1999) Acta Cryst. D55, An introduction to data reduction: space-group determination, scaling and intensity statistics P. R. Evans (2011) Acta Cryst. D67,
36 Outlook anisotropy: elliptic cutoff or use all data? a refinement program that does not use experimental sigmas suffers from noise amplification, and benefits from throwing away data in the weak directions phenix.refine does not use the experimental sigmas; Refmac and CNS do.
37 How to obtain good data, given a total dose Old/classic/ conservative better Statistics Rmerge CC1/2 Exposure Reflections visible; tolerate some overloads Low-dose, high multiplicity Oscillation range 1 Pilatus: CCD: Rotation range strategy, xplan 180 /360 native/anomalous
Data quality indicators. Kay Diederichs
Data quality indicators Kay Diederichs Crystallography has been highly successful Now 105839 Could it be any better? 2 Confusion what do these mean? CC1/2 Rmerge Rsym Mn(I/sd) I/σ Rmeas CCanom Rpim Rcum
More informationData quality noise, errors, mistakes
Data quality noise, errors, mistakes Kay Diederichs Protein Crystallography / Molecular Bioinformatics University of Konstanz, Germany Crystallography has been extremely successful Protein Data Bank on
More informationResolution and data formats. Andrea Thorn
Resolution and data formats Andrea Thorn RESOLUTION Motivation Courtesy of M. Sawaya Map resolution http://www.bmsc.washington.edu/people/verlinde/experiment.html Data quality indicators Resolution accounts
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 informationQuantifying instrument errors in macromolecular X-ray data sets
Acta Crystallographica Section D Biological Crystallography ISSN 0907-4449 Editors: E. N. Baker and Z. Dauter Quantifying instrument errors in macromolecular X-ray data sets Kay Diederichs Acta Cryst.
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 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 informationDiffraction Geometry
Diffraction Geometry Diffraction from a crystal - Laue equations Reciprocal lattice Ewald construction Data collection strategy Phil Evans LMB May 2013 MRC Laboratory of Molecular Biology Cambridge UK
More informationTwinning in PDB and REFMAC. Garib N Murshudov Chemistry Department, University of York, UK
Twinning in PDB and REFMAC Garib N Murshudov Chemistry Department, University of York, UK Contents Crystal peculiarities Problem of twinning Occurrences of twinning in PDB Recognition of potential operators
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 informationRNA protects a nucleoprotein complex against radiation damage
Supporting information Volume 72 (2016) Supporting information for article: RNA protects a nucleoprotein complex against radiation damage Charles S. Bury, John E. McGeehan, Alfred A. Antson, Ian Carmichael,
More informationData Reduction. Space groups, scaling and data quality. MRC Laboratory of Molecular Biology Cambridge UK. Phil Evans Diamond December 2017
Data Reduction Space groups, scaling and data quality Phil Evans Diamond December 2017 MRC Laboratory of Molecular Biology Cambridge UK F 2 Scaling and Merging Experiment lots of effects ( errors ) I Our
More informationX-ray Data Collection. Bio5325 Spring 2006
X-ray Data Collection Bio535 Spring 006 Obtaining I hkl and α (Ihkl) from Frame Images Braggs Law -predicts conditions for in-phase scattering by equivalent atoms lying in planes that transect a crystal.
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 informationAnisotropy in macromolecular crystal structures. Andrea Thorn July 19 th, 2012
Anisotropy in macromolecular crystal structures Andrea Thorn July 19 th, 2012 Motivation Courtesy of M. Sawaya Motivation Crystal structures are inherently anisotropic. X-ray diffraction reflects this
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 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 informationCalculating strategies for data collection
Calculating strategies for data collection Alexander Popov A.Popov 1 Data quality Completeness, Resolution, Statistics Detector Size Size N.of N.of pixels pixels T T readout readout Noise Noise Sensitivity
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 informationresearch papers Detecting outliers in non-redundant diffraction data 1. Introduction Randy J. Read
Acta Crystallographica Section D Biological Crystallography ISSN 0907-4449 Detecting outliers in non-redundant diffraction data Randy J. Read Department of Haematology, University of Cambridge, Cambridge
More informationHigh-resolution crystal structure of ERAP1 with bound phosphinic transition-state analogue inhibitor
High-resolution crystal structure of ERAP1 with bound phosphinic transition-state analogue inhibitor Petros Giastas 1, Margarete Neu 2, Paul Rowland 2, and Efstratios Stratikos 1 1 National Center for
More informationExperimental Phasing of SFX Data. Thomas Barends MPI for Medical Research, Heidelberg. Conclusions
Experimental Phasing of SFX Data Thomas Barends MP for Medical Researc Heidelberg Conclusions X-ray Free-Electron Lasers are pushing back the boundaries of possibility in biological crystallography: -Data
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 informationElectronic Supplementary Information (ESI) for Chem. Commun. Unveiling the three- dimensional structure of the green pigment of nitrite- cured meat
Electronic Supplementary Information (ESI) for Chem. Commun. Unveiling the three- dimensional structure of the green pigment of nitrite- cured meat Jun Yi* and George B. Richter- Addo* Department of Chemistry
More informationHow To Evaluate Electron Crystallographic Data
How To Evaluate Electron Crystallographic Data Vinzenz Unger, Dept of Molecular Biosciences, Northwestern University Chemistry of Life Sciences Institute, Northwestern University Unstained = Resolution
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 informationRecognition of the amber UAG stop codon by release factor RF1
Manuscript EMBO-2010-73984 Recognition of the amber UAG stop codon by release factor RF1 Andrei Korostelev, Jianyu Zhu, Haruichi Asahara and Harry F. Noller Corresponding author: Harry F. Noller, Univ.
More informationNon-merohedral Twinning in Protein Crystallography
Bruker Users Meeting 2010 Karlsruhe, 22 nd September 2010 Non-merohedral Twinning in Protein Crystallography Regine Herbst-Irmer rherbst@shelx.uni-ac.gwdg.de http://shelx.uni-ac.gwdg.de/~rherbst/twin.html
More informationUltra-high resolution structures in validation
Ultra-high resolution structures in validation (and not only...) Mariusz Jaskolski Department of Crystallography,, A. Mickiewicz University Center for Biocrystallographic Research, Polish Academy of Sciences,
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 informationPAN-modular Structure of Parasite Sarcocystis muris Microneme Protein SML-2 at 1.95 Å Resolution and the Complex with 1-Thio-β-D-Galactose
Supplementary Material to the paper: PAN-modular Structure of Parasite Sarcocystis muris Microneme Protein SML-2 at 1.95 Å Resolution and the Complex with 1-Thio-β-D-Galactose Jürgen J. Müller, a Manfred
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 informationGC376 (compound 28). Compound 23 (GC373) (0.50 g, 1.24 mmol), sodium bisulfite (0.119 g,
Supplemental Material Synthesis of GC376 GC376 (compound 28). Compound 23 (GC373) (0.50 g, 1.24 mmol), sodium bisulfite (0.119 g, 1.12 mmol), ethyl acetate (2 ml), ethanol (1 ml) and water (0.40 ml) were
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 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 informationEnsemble refinement of protein crystal structures in PHENIX. Tom Burnley Piet Gros
Ensemble refinement of protein crystal structures in PHENIX Tom Burnley Piet Gros Incomplete modelling of disorder contributes to R factor gap Only ~5% of residues in the PDB are modelled with more than
More informationSUPPLEMENTARY INFORMATION
DOI: 10.1038/NCHEM.1397 Crystal structures of Λ-[Ru(phen) 2 dppz] 2+ with oligonucleotides containing TA/TA and AT/AT steps show two intercalation modes Hakan Niyazi a, 1 James P. Hall a, Kyra O Sullivan
More informationExperimental Phasing with SHELX C/D/E
WIR SCHAFFEN WISSEN HEUTE FÜR MORGEN Dr. Tim Grüne :: Paul Scherrer Institut :: tim.gruene@psi.ch Experimental Phasing with SHELX C/D/E CCP4 / APS School Chicago 2017 22 nd June 2017 1 - The Phase Problem
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 informationSUPPLEMENTARY INFORMATION
Supplementary Table 1: Amplitudes of three current levels. Level 0 (pa) Level 1 (pa) Level 2 (pa) TrkA- TrkH WT 200 K 0.01 ± 0.01 9.5 ± 0.01 18.7 ± 0.03 200 Na * 0.001 ± 0.01 3.9 ± 0.01 12.5 ± 0.03 200
More informationChanging and challenging times for service crystallography. Electronic Supplementary Information
Changing and challenging times for service crystallography Simon J Coles,* a and Philip A Gale* a Electronic Supplementary Information Instrument descriptions and experimental protocols The following firstly
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 informationSOLVE and RESOLVE: automated structure solution, density modification and model building
Journal of Synchrotron Radiation ISSN 0909-0495 SOLVE and RESOLVE: automated structure solution, density modification and model building Thomas Terwilliger Copyright International Union of Crystallography
More information8:10 pm Keynote Lecture: Michael G. Rossmann, Purdue University Current challenges in structural biology
Sunday, October 11 3:00 pm Check-in 6:00 pm Reception (Lobby) 7:00 pm Dinner 8:00 pm Introductory Notes: Tamir Gonen 8:10 pm Keynote Lecture: Michael G. Rossmann, Purdue University Current challenges in
More informationElectron Crystallography for Structure Solution Latest Results from the PSI Electron Diffraction Group
WIR SCHAFFEN WISSEN HEUTE FÜR MORGEN Dr. Tim Grüne :: Paul Scherrer Institut :: tim.gruene@psi.ch Electron Crystallography for Structure Solution Latest Results from the PSI Electron Diffraction Group
More informationSUPPLEMENTARY INFORMATION
Table of Contents Page Supplementary Table 1. Diffraction data collection statistics 2 Supplementary Table 2. Crystallographic refinement statistics 3 Supplementary Fig. 1. casic1mfc packing in the R3
More informationSI Text S1 Solution Scattering Data Collection and Analysis. SI references
SI Text S1 Solution Scattering Data Collection and Analysis. The X-ray photon energy was set to 8 kev. The PILATUS hybrid pixel array detector (RIGAKU) was positioned at a distance of 606 mm from the sample.
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 informationActa Crystallographica Section F
Supporting information Acta Crystallographica Section F Volume 70 (2014) Supporting information for article: Chemical conversion of cisplatin and carboplatin with histidine in a model protein crystallised
More informationX-Ray Damage to Biological Crystalline Samples
X-Ray Damage to Biological Crystalline Samples Gerd Rosenbaum Structural Biology Center, ANL and Dept. of Biochemistry, UGA ACA Summer School IIT, 19 July 2007 A U.S. Department of Energy laboratory managed
More informationData processing and reduction
Data processing and reduction Leopoldo Suescun International School on Fundamental Crystallography 2014 May 1st, 2014 Reciprocal lattice c* b* b * dh' k' l' 1 dh' k' l' * dhkl 1 dhkl a a* 0 d hkl c bc
More informationThe structure of Aquifex aeolicus FtsH in the ADP-bound state reveals a C2-symmetric hexamer
Volume 71 (2015) Supporting information for article: The structure of Aquifex aeolicus FtsH in the ADP-bound state reveals a C2-symmetric hexamer Marina Vostrukhina, Alexander Popov, Elena Brunstein, Martin
More informationTable S1. Overview of used PDZK1 constructs and their binding affinities to peptides. Related to figure 1.
Table S1. Overview of used PDZK1 constructs and their binding affinities to peptides. Related to figure 1. PDZK1 constru cts Amino acids MW [kda] KD [μm] PEPT2-CT- FITC KD [μm] NHE3-CT- FITC KD [μm] PDZK1-CT-
More informationPractical aspects of SAD/MAD. Judit É Debreczeni
Practical aspects of SAD/MAD Judit É Debreczeni anomalous scattering Hg sinθ/λ CuKα 0 Å - 0.4 Å - 0.6 Å - Å.5Å 0.83Å f 80 53 4 f total (θ, λ) f(θ) + f (λ) + if (λ) f f -5 8-5 8-5 8 f total increasing with
More informationSupporting Information. Full and Partial Agonism of a Designed Enzyme Switch
Supporting Information Full and Partial Agonism of a Designed Enzyme Switch S. Jimmy Budiardjo 1, Timothy J. Licknack 2, Michael B. Cory 2, Dora Kapros 2, Anuradha Roy 3, Scott Lovell 4, Justin Douglas
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 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 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 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 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 informationActa Cryst. (2017). D73, doi: /s
Acta Cryst. (2017). D73, doi:10.1107/s2059798317010932 Supporting information Volume 73 (2017) Supporting information for article: Designing better diffracting crystals of biotin carboxyl carrier protein
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 informationTutorial on how to solve a Se-substructure using
1 Introduction Tutorial on how to solve a Se-substructure using SHELXD Thomas R. Schneider Dept. of Structural Chemistry University of Göttingen trs@shelx.uni-ac.gwdg.de July 4, 2002 The Solution of the
More informationSpace Group & Structure Solution
Space Group & Structure Solution Determine the Space Group Space group determination can always be performed by hand by examining the intensity data. A program that can facilitate this step is the command-prompt
More informationresearch papers HKL-3000: the integration of data reduction and structure solution from diffraction images to an initial model in minutes
Acta Crystallographica Section D Biological Crystallography ISSN 0907-4449 HKL-3000: the integration of data reduction and structure solution from diffraction images to an initial model in minutes Wladek
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 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 informationProtein 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 informationStructure solution from weak anomalous data
Structure solution from weak anomalous data Phenix Workshop SBGrid-NE-CAT Computing School Harvard Medical School, Boston June 7, 2014 Gábor Bunkóczi, Airlie McCoy, Randy Read (Cambridge University) Nat
More informationMacromolecular Crystallography Part II
Molecular Biology Course 2010 Macromolecular Crystallography Part II University of Göttingen Dept. of Structural Chemistry November 2010 http://shelx.uni-ac.gwdg.de tg@shelx.uni-ac.gwdg.de Crystallography
More informationSupporting Information
Wiley-VCH 2007 69451 Weinheim, Germany On the polymorphism of aspirin Andrew D. Bond, Roland Boese and Gautam R. Desiraju S1. Comparison of the form I and PZ structures S2. Transforming the unit cells
More informationCSE 417T: Introduction to Machine Learning. Final Review. Henry Chai 12/4/18
CSE 417T: Introduction to Machine Learning Final Review Henry Chai 12/4/18 Overfitting Overfitting is fitting the training data more than is warranted Fitting noise rather than signal 2 Estimating! "#$
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 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 informationThe Growth of Functions. A Practical Introduction with as Little Theory as possible
The Growth of Functions A Practical Introduction with as Little Theory as possible Complexity of Algorithms (1) Before we talk about the growth of functions and the concept of order, let s discuss why
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 informationSupplemental Data. Structure of the Rb C-Terminal Domain. Bound to E2F1-DP1: A Mechanism. for Phosphorylation-Induced E2F Release
Supplemental Data Structure of the Rb C-Terminal Domain Bound to E2F1-DP1: A Mechanism for Phosphorylation-Induced E2F Release Seth M. Rubin, Anne-Laure Gall, Ning Zheng, and Nikola P. Pavletich Section
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 informationPsychology Seminar Psych 406 Dr. Jeffrey Leitzel
Psychology Seminar Psych 406 Dr. Jeffrey Leitzel Structural Equation Modeling Topic 1: Correlation / Linear Regression Outline/Overview Correlations (r, pr, sr) Linear regression Multiple regression interpreting
More informationImage Assessment San Diego, November 2005
Image Assessment San Diego, November 005 Pawel A. Penczek The University of Texas Houston Medical School Department of Biochemistry and Molecular Biology 6431 Fannin, MSB6.18, Houston, TX 77030, USA phone:
More information5.067 Crystal Structure Refinement Fall 2007
MIT OpenCourseWare http://ocw.mit.edu 5.067 Crystal Structure Refinement Fall 2007 For information about citing these materials or our Terms of Use, visit: http://ocw.mit.edu/terms. Artefacts An artefact
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 informationSynthesis of Tetra-ortho-Substituted, Phosphorus- Containing and Carbonyl-Containing Biaryls Utilizing a Diels-Alder Approach
Synthesis of Tetra-ortho-Substituted, Phosphorus- Containing and Carbonyl-Containing Biaryls Utilizing a Diels-Alder Approach Bradley O. Ashburn and Rich G. Carter* and Lev N. Zakharov Department of Chemistry,
More informationClassification and Regression Trees
Classification and Regression Trees Ryan P Adams So far, we have primarily examined linear classifiers and regressors, and considered several different ways to train them When we ve found the linearity
More informationS-SAD and Fe-SAD Phasing using X8 PROTEUM
S-SAD and Fe-SAD Phasing using X8 PROTEUM Kristina Djinovic Carugo Dept. for Structural and Computational Biology Max F. Perutz Labs Univ. Vienna, Austria Outline Fe-SAD on chlorite dismutase from Candidatus
More informationHigh Fidelity to Low Weight. Daniel Gottesman Perimeter Institute
High Fidelity to Low Weight Daniel Gottesman Perimeter Institute A Word From Our Sponsor... Quant-ph/0212066, Security of quantum key distribution with imperfect devices, D.G., H.-K. Lo, N. Lutkenhaus,
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 informationModel Accuracy Measures
Model Accuracy Measures Master in Bioinformatics UPF 2017-2018 Eduardo Eyras Computational Genomics Pompeu Fabra University - ICREA Barcelona, Spain Variables What we can measure (attributes) Hypotheses
More informationStatistical inference
Statistical inference Contents 1. Main definitions 2. Estimation 3. Testing L. Trapani MSc Induction - Statistical inference 1 1 Introduction: definition and preliminary theory In this chapter, we shall
More informationHigh-Throughput in Chemical Crystallography from an industrial point of view
High-Throughput in Chemical Crystallography from an industrial point of view Ina Dix Novartis Institutes for Biomedical Research, Basel Analytics at Novartis (Basel) staff # spectra NMR 8 10.000 1.500
More informationCase Studies in Molecular Replacement
Case Studies in Molecular Replacement Melanie Vollmar Structural Genomics Consortium University of Oxford SGC Toronto SGC Oxford SGC Stockholm Overview Information about target protein Tools for model
More informationRemote Asymmetric Induction in an Intramolecular Ionic Diels-Alder Reaction: Application to the Total Synthesis of (+)-Dihydrocompactin
Page S16 Remote Asymmetric Induction in an Intramolecular Ionic Diels-Alder Reaction: Application to the Total Synthesis of (+)-Dihydrocompactin Tarek Sammakia,* Deidre M. Johns, Ganghyeok Kim, and Martin
More informationA Primer in X-ray Crystallography for Redox Biologists. Mark Wilson Karolinska Institute June 3 rd, 2014
A Primer in X-ray Crystallography for Redox Biologists Mark Wilson Karolinska Institute June 3 rd, 2014 X-ray Crystallography Basics Optimistic workflow for crystallography Experiment Schematic Fourier
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 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 informationA tutorial for learning and teaching macromolecular crystallography
A tutorial for learning and teaching macromolecular crystallography Annette Faust, Santosh Panjikar, Uwe Mueller, Venkataraman Parthasarathy, Andrea Schmidt, Victor S. Lamzin and Manfred S. Weiss Reference:
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 informationStep 1 Determine the Order of the Reaction
Step 1 Determine the Order of the Reaction In this step, you fit the collected data to the various integrated rate expressions for zezro-, half-, first-, and second-order kinetics. (Since the reaction
More informationHow to use the simulator
How to use the simulator Overview The application allows for the exploration of four quantum circuits in all. Each simulator grants the user a large amount of freedom in experments they wish to conduct.
More information