Electron Crystallography for Structure Solution Latest Results from the PSI Electron Diffraction Group
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1 WIR SCHAFFEN WISSEN HEUTE FÜR MORGEN Dr. Tim Grüne :: Paul Scherrer Institut :: Electron Crystallography for Structure Solution Latest Results from the PSI Electron Diffraction Group Research Complex at Harwell Seminars 13 th April 2017
2 1 - Crystallography under the Microscope Instrumentation available at C CINA, University Basel 1. FEI Polara, 200keV, 512x512 Timepix detector, single axis ±30 2. FEI Talos, 200keV, 1024x1024 Timepix detector, single axis ±40 RCa Harwell Seminars 13 th April /34
3 The Lens System Gun / Source C Objective lens C2 C3 Sample Lenses C1 C3 shape beam Crystallography: Parallel beam Objective lens: sets effective detector distance to backfocal plane = diffraction mode C3 not present in all microscopes Lenses cause distortions. Diffraction Plane Imaging Plane RCa Harwell Seminars 13 th April /34
4 Electron Microscope: Imaging Mode Plane Wave Object Lense Image Plane (Detector) Rays of equal origin focus on detector RCa Harwell Seminars 13 th April /34
5 Electron Microscope: Imaging Mode Detector noise and radiation senstivity require low contrast images Plane Wave Object Lense Image Plane (Detector) Martinez-Rucobo et al. Molecular Cell (2015) 58, RCa Harwell Seminars 13 th April /34
6 Electron Microscope: Diffraction Mode Plane Wave Object Lense RCa Harwell Seminars 13 th April /34
7 Electron Microscope: Diffraction Mode Image at Backfocal Plane = Fouriertransform of object If object = crystal: diffraction spots according to Laue conditions Backfocal Plane Rays of equal direction focus on detector Plane Wave Object Lense RCa Harwell Seminars 13 th April /34
8 2 - Experimental Considerations 1. Ewald sphere: refinement stability 2. Dynamic scattering 3. Detectors RCa Harwell Seminars 13 th April /34
9 X rays: The Ewald Sphere λ = 1Å, normal resolution: 2θ max = 40 1/λ correct distance incorrect distance Assume: wrong detector distance Diffraction spot calculated wrongly (red circle) Reciprocal lattice becomes distorted Curvature of the Ewald sphere gauges the diffraction geometry RCa Harwell Seminars 13 th April /34
10 Electrons: The Ewald Plane 1/λ e = 1/0.025Å 1/λ X = 1/1Å Typical X ray wavelength λ X = 1Å Typical e wavelength λ e = 0.025Å Radius of Ewald sphere 40x greater Ewald sphere nearly flat RCa Harwell Seminars 13 th April /34
11 Electrons: The Ewald Plane 1/λ e = 1/0.025Å normal resolution: 2θ max = 1 typical wavelength with X rays: 1Å typical wavelength with electrons: 0.025Å opening angle 1 4 Ewald sphere virtually flat Without curvature: impossible to refine both detector distance and cell RCa Harwell Seminars 13 th April /34
12 Summary: The Ewald Plane Detector distance and unit cell parameters are strongly related Wrongly set distance can lead to incorrect bond lengths Distance refinement with X ray data routine Distance refinement with electron data = unstable good: Distance calibration from powder sample better: Distance calibration from chemical bond lengths RCa Harwell Seminars 13 th April /34
13 Dynamic Scattering Kinematic Theory of Diffraction: Every photon / electron / neutron scatters once in the crystal F ideal (hkl) I exp (hkl) Dynamic Scattering: Multiple Scattering events occur Electron Diffraction: Multiple Scattering occurs even with nanocrystals RCa Harwell Seminars 13 th April /34
14 Dynamic Scattering Data from SAPO 34: I( 2, 1,1)>I direct beam (Eiger chip, 256x256 px) RCa Harwell Seminars 13 th April /34
15 Multiple (Dual) Scattering S i Outgoing ray S o 1 acts as incoming ray for reflection S o 2. Probability of re reflection thickness dependent S 1 o S 2 o RCa Harwell Seminars 13 th April /34
16 Multiple (Dual) Scattering Laue Conditions (accordingly b and c): S i S 1 o ( S 1 o S i ) a=h 1 ( S 2 o S 1 o) a=h ( S 2 o S i ) a=h 1 + h = h 2 S 2 o S 2 o Requirement for detrimental effect on I(h 2,k 2,l 2 ) I(h 1 k 1 l 1 ) must be strong I(h,k,l ) must be strong I(h 2 k 2 l 2 ) must be weak I(h 1 k 1 l 1 ) and I(h 2 k 2 l 2 ) on same frame RCa Harwell Seminars 13 th April /34
17 Multiple (Dual) Scattering I(hkl) I(h 1 k 1 l 1 ) I(h 2 k 2 l 2 ) Re-reflection more likely for thicker crystal(path) Percentage similar for all reflections on frame (2θ 0) 10% of strong reflection affects weak reflection Measured intensities shifted from strong to weak Low resolution reflection under, high resolution reflections overestimated Covered during refinement by reduced B factor: electron diffraction includes map sharpening RCa Harwell Seminars 13 th April /34
18 e Diffraction Studies with Timepix and Eiger TVIPS CMOS 1024x1024 Timepix 256x256 Eiger (PSI) 20 I 21 cts 0 I 1 ct Lysozyme (inv d ) 0 I 1 ct SAPO 34 crystal 1kHz,50µm 50µm 23kHz,75µm 75µm cut off: cut off: 16, 64, or 4096 (4, 8, 12 bit) dead time 0.01s dead time 3µs RCa Harwell Seminars 13 th April /34
19 3 - Structures RCa Harwell Seminars 13 th April /34
20 Pharmaceutical I: Visualisation of Hydrogen Atoms H atom positions can be refined against electron diffraction data CCDC: IRELOH, Dai et al., Eur. J. Org. Chem (2010), Sample courtesy Novartis Field of view: 3µm Crystal: 1.6µm 400nm d min < 0.8Å P : 85% completeness with 3 crystals a=8.06å b=10.00å c=17.73å Hydrogen atoms in difference map even with poor model 1334 reflections, 195 parameters, 156 restraints (RIGU) R1=15.5%,R complete = 18.5% RCa Harwell Seminars 13 th April /34
![Pharmaceutical II: Differentiation of Atom Types Data quality: recognition of atom types, C vs. O vs. N etc. (CCDC: EPICZA) d [Å] 5 2.5 1.](/docs-images/74/70102895/images/21-0.jpg "25 1.0 Completeness [%] 100 80 60 40 20 0 Completeness I/σ I 12 11 10 9 8 7 6 5 4 3 2 I/σ I 0 0.1 0.2 0.3 0.4 0.5 0.")
![6 d* [1/Å] Field of view: 3µm Crystal: 400nm diameter d min = 0.87Å a=11.35å, b=12.7å, c=13.](/docs-images/74/70102895/images/21-1.jpg "0å P2 1 2 1 2 1 : completeness with 4 crystals: 86% 2545 refl., 258 param., 267 restraints (RIGU) all data: R1=15.9%,R complete = 19.")
21 Pharmaceutical II: Differentiation of Atom Types Data quality: recognition of atom types, C vs. O vs. N etc. (CCDC: EPICZA) d [Å] Completeness [%] Completeness I/σ I I/σ I d* [1/Å] Field of view: 3µm Crystal: 400nm diameter d min = 0.87Å a=11.35å, b=12.7å, c=13.0å P : completeness with 4 crystals: 86% 2545 refl., 258 param., 267 restraints (RIGU) all data: R1=15.9%,R complete = 19.1% R1=14.7%,R complete = 18.0% RCa Harwell Seminars 13 th April /34
22 Pharmaceutical II (EPICZA): Structure Solution Process Direct methods reveal H atoms HFIX: all except 1 H Final Structure =data quality =model quality RCa Harwell Seminars 13 th April /34
23 Summary: Electron Diffraction of Organic Compounds Structures can be solved with X ray knowledge and methods. Radiation damage present, but not (always) limiting Kinematic approximation sufficient for high quality structures IRELOH EPICZA Bond lengths X model [Å] x line fit f(x) = 0.92 * x e-01 Bond lengths X-ray model [Å] x line fit f(x) = 0.96 * x e Bond lengths e - model [Å] Bond lengths e - model [Å] RCa Harwell Seminars 13 th April /34
24 Thermolysin (sample courtesy Ilme Schlichting) Spacegroup P Unit Cell d min = 3.5Å 72.4% completeness MR with 3DNZ poly Alanine: TFZ=26.4, LLG=433 Buccaneer: side chain extension 315/316 Refmac5: R1/ Rfree = 28.0% / 29.9% (4N5P w/o water) RCa Harwell Seminars 13 th April /34
25 Summary: Electron Diffraction of Proteins Structures can be solved with X ray knowledge and methods. Kinematic approximation sufficient for high quality structures Radiation damage major limit Possibility: serial electron crystallography RCa Harwell Seminars 13 th April /34
26 4 - Crystallographic Lens Corrections RCa Harwell Seminars 13 th April /34
27 Garnet Andradite The garnet Andradite, Ca 3 Fe 2 3+ (SiO 4 ) 3, radiation hard 2 grids courtesy Xiaodong Zou (Stockholm) Space group Ia 3d, a= (1)å (ICSD No ) (Wikipedia) Summed images from Garnet (200keV) 66.8 rotation good coverage of detector surface RCa Harwell Seminars 13 th April /34
28 Spatial Correction for the Detector Surface XDS Correction Table X coordinate Spot positions determined through Laue Conditions S. a=h S. b=k S. c=l +10 Deviations between calculated and observed positions per pixel look-up tables for X and Y coordinates Independent of Source of Error -5 RCa Harwell Seminars 13 th April /34
29 Directly Visible Improvements Garnet Data set processed before spatial correction: BEAM DIVERGENCE: 0.16 REFLECTING RANGE: 0.47 Garnet Data set processed after spatial correction: BEAM DIVERGENCE: 0.15 REFLECTING RANGE: 0.28 RCa Harwell Seminars 13 th April /34
30 Improved Cell Accuracy with Look up Tables 1. Collect data from garnet 2. Change as little as possible 3. Collect data from target sample 4. Process using garnet correction tables Sample Courtesy Roche C 31 H 29 Cl 2 F 2 N 3 O 4, SG P2 1 Data Collection and Processing: Max Clabbers a b c α β γ XRPD XDS uncorrected XDS corrected RCa Harwell Seminars 13 th April /34
31 5 - Data Processing RCa Harwell Seminars 13 th April /34
32 Integration with XDS XDS (W. Kabsch, K. Diederichs) for data integration and scaling Profile fitting: extraction of weak data Versatile geometry Detector segmentation Refinement of experimental params: 1. Detector distance Unit cell 2. Cell orientation 3. (Beam position) 4. Rotation axis 5. Reflecting range REFINED VALUES OF DIFFRACTION PARAMETERS DERIVED FROM 1134 INDEXED SPOTS REFINED PARAMETERS: AXIS BEAM ORIENTATION CELL STANDARD DEVIATION OF SPOT POSITION (PIXELS) 0.89 STANDARD DEVIATION OF SPINDLE POSITION (DEGREES) 0.34 SPACE GROUP NUMBER 1 UNIT CELL PARAMETERS E.S.D. OF CELL PARAMETERS 3.1E E E E E E-01 REC. CELL PARAMETERS COORDINATES OF UNIT CELL A-AXIS COORDINATES OF UNIT CELL B-AXIS COORDINATES OF UNIT CELL C-AXIS CRYSTAL MOSAICITY (DEGREES) LAB COORDINATES OF ROTATION AXIS DIRECT BEAM COORDINATES (REC. ANGSTROEM) DETECTOR COORDINATES (PIXELS) OF DIRECT BEAM DETECTOR ORIGIN (PIXELS) AT CRYSTAL TO DETECTOR DISTANCE (mm) LAB COORDINATES OF DETECTOR X-AXIS LAB COORDINATES OF DETECTOR Y-AXIS RCa Harwell Seminars 13 th April /34
33 Downstream of Processing Scaling: part of XDS (single data set) Merging: XSCALE (no overfitting of σ s), sadabs (higher outlier rejection) SHELXT / SHELXD unmodified Phaser / Buccaneer unmodified Refinement: SHELXL (electron scattering factors e.g. Peng et al. (1996)) Refmac5: SOURCE ELECTRON MB (Mott-Bethe);MAPC FREE EXCLUDE in principle like D. Dorset (1992), but easier and faster RCa Harwell Seminars 13 th April /34
34 6 - Conclusions 200keV C1 C2 C3 Horizontal tube: better space, more stable goniometer Fixed Voltage Thin tube C3 lens system: parallel beam 360 Vertical Goniometer (precision, contact cooling) Detector moveable RCa Harwell Seminars 13 th April /34
35 7 - Acknowledgements Prof. J. P. Abrahams, Dr. E. van Genderen, M. Clabbers, Dr. T. Blum, C. Borsa, J. Heidler, Dr. R. Pantelic Novartis (Compounds) Roche (Compounds) Dr. I. Nederlof, ASI (Medipix / Timepix) Dr. B. Schmitt, PSI Detector group Prof. K. Diederichs (XDS) Dr. W. Kabsch (XDS) Dr. D. Waterman (DIALS) Prof. J. van Bokhoven, ETH Zürich Prof. X. Zou and S. Hovmöller, University Stockholm (garnet grids) RCa Harwell Seminars 13 th April /34
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