OSTI.GOV Journal Article: A revised partiality model and post-refinement algorithm for X-ray free-electron laser data
Title: A revised partiality model and post-refinement algorithm for X-ray free-electron laser data
An updated partiality model and post-refinement algorithm for XFEL snapshot diffraction data is presented and confirmed by observing anomalous density for S atoms at an X-ray wavelength of 1.3 Å. Research towards using X-ray free-electron laser (XFEL) data to solve structures using experimental phasing methods such as sulfur single-wavelength anomalous dispersion (SAD) has been hampered by shortcomings in the diffraction models for X-ray diffraction from FELs. Owing to errors in the orientation matrix and overly simple partiality models, researchers have required large numbers of images to converge to reliable estimates for the structure-factor amplitudes, which may not be feasible for all biological systems. Here, data for cytoplasmic polyhedrosis virus type 17 (CPV17) collected at 1.3 Å wavelength at the Linac Coherent Light Source (LCLS) are revisited. A previously published definition of a partiality model for reflections illuminated by self-amplified spontaneous emission (SASE) pulses is built upon, which defines a fraction between 0 and 1 based on the intersection of a reflection with a spread of Ewald spheres modelled by a super-Gaussian wavelength distribution in the X-ray beam. A method of post-refinement to refine the parameters of this model is suggested. This has generated a merged data set with an overallmore » discrepancy (by calculating the R{sub split} value) of 3.15% to 1.46 Å resolution from a 7225-image data set. The atomic numbers of C, N and O atoms in the structure are distinguishable in the electron-density map. There are 13 S atoms within the 237 residues of CPV17, excluding the initial disordered methionine. These only possess 0.42 anomalous scattering electrons each at 1.3 Å wavelength, but the 12 that have single predominant positions are easily detectable in the anomalous difference Fourier map. It is hoped that these improvements will lead towards XFEL experimental phase determination and structure determination by sulfur SAD and will generally increase the utility of the method for difficult cases.« less
Ginn, Helen Mary [1]; Brewster, Aaron S.; Hattne, Johan [2]; Evans, Gwyndaf; Wagner, Armin [3]; Grimes, Jonathan M. [1]; Sauter, Nicholas K. [2]; Sutton, Geoff [1]
Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7BN (United Kingdom)
Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720 (United States)
Harwell Science and Innovation Campus, Fermi Avenue, Didcot OX11 0QX (United Kingdom)
Acta Crystallographica. Section D: Biological Crystallography
Journal Volume: 71; Journal Issue: Pt 6; Other Information: PMCID: PMC4461207; PMID: 26057680; PUBLISHER-ID: dz5368; OAI: oai:pubmedcentral.nih.gov:4461207; Copyright (c) Ginn et al. 2015; This is an open-access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are cited.; Country of input: International Atomic Energy Agency (IAEA); Journal ID: ISSN 0907-4449
71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSICS; 75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND SUPERFLUIDITY; ALGORITHMS; AMPLITUDES; ATOMS; DENSITY; DISTRIBUTION; ELECTRON DENSITY; ELECTRONS; ERRORS; IMAGES; MATRICES; PULSES; SCATTERING; SPHERES; WAVELENGTHS
Ginn, Helen Mary, Brewster, Aaron S., Hattne, Johan, Evans, Gwyndaf, Wagner, Armin, Grimes, Jonathan M., Harwell Science and Innovation Campus, Fermi Avenue, Didcot OX11 0QX, Sauter, Nicholas K., Sutton, Geoff, Stuart, David Ian, E-mail: dave@strubi.ox.ac.uk, and Harwell Science and Innovation Campus, Fermi Avenue, Didcot OX11 0QX. A revised partiality model and post-refinement algorithm for X-ray free-electron laser data. Denmark: N. p., 2015. Web. doi:10.1107/S1399004715006902.
Ginn, Helen Mary, Brewster, Aaron S., Hattne, Johan, Evans, Gwyndaf, Wagner, Armin, Grimes, Jonathan M., Harwell Science and Innovation Campus, Fermi Avenue, Didcot OX11 0QX, Sauter, Nicholas K., Sutton, Geoff, Stuart, David Ian, E-mail: dave@strubi.ox.ac.uk, & Harwell Science and Innovation Campus, Fermi Avenue, Didcot OX11 0QX. A revised partiality model and post-refinement algorithm for X-ray free-electron laser data. Denmark. doi:10.1107/S1399004715006902.
Ginn, Helen Mary, Brewster, Aaron S., Hattne, Johan, Evans, Gwyndaf, Wagner, Armin, Grimes, Jonathan M., Harwell Science and Innovation Campus, Fermi Avenue, Didcot OX11 0QX, Sauter, Nicholas K., Sutton, Geoff, Stuart, David Ian, E-mail: dave@strubi.ox.ac.uk, and Harwell Science and Innovation Campus, Fermi Avenue, Didcot OX11 0QX. Sat . "A revised partiality model and post-refinement algorithm for X-ray free-electron laser data". Denmark. doi:10.1107/S1399004715006902.
@article{osti_22389069,
title = {A revised partiality model and post-refinement algorithm for X-ray free-electron laser data},
author = {Ginn, Helen Mary and Brewster, Aaron S. and Hattne, Johan and Evans, Gwyndaf and Wagner, Armin and Grimes, Jonathan M. and Harwell Science and Innovation Campus, Fermi Avenue, Didcot OX11 0QX and Sauter, Nicholas K. and Sutton, Geoff and Stuart, David Ian, E-mail: dave@strubi.ox.ac.uk and Harwell Science and Innovation Campus, Fermi Avenue, Didcot OX11 0QX},
abstractNote = {An updated partiality model and post-refinement algorithm for XFEL snapshot diffraction data is presented and confirmed by observing anomalous density for S atoms at an X-ray wavelength of 1.3 Å. Research towards using X-ray free-electron laser (XFEL) data to solve structures using experimental phasing methods such as sulfur single-wavelength anomalous dispersion (SAD) has been hampered by shortcomings in the diffraction models for X-ray diffraction from FELs. Owing to errors in the orientation matrix and overly simple partiality models, researchers have required large numbers of images to converge to reliable estimates for the structure-factor amplitudes, which may not be feasible for all biological systems. Here, data for cytoplasmic polyhedrosis virus type 17 (CPV17) collected at 1.3 Å wavelength at the Linac Coherent Light Source (LCLS) are revisited. A previously published definition of a partiality model for reflections illuminated by self-amplified spontaneous emission (SASE) pulses is built upon, which defines a fraction between 0 and 1 based on the intersection of a reflection with a spread of Ewald spheres modelled by a super-Gaussian wavelength distribution in the X-ray beam. A method of post-refinement to refine the parameters of this model is suggested. This has generated a merged data set with an overall discrepancy (by calculating the R{sub split} value) of 3.15% to 1.46 Å resolution from a 7225-image data set. The atomic numbers of C, N and O atoms in the structure are distinguishable in the electron-density map. There are 13 S atoms within the 237 residues of CPV17, excluding the initial disordered methionine. These only possess 0.42 anomalous scattering electrons each at 1.3 Å wavelength, but the 12 that have single predominant positions are easily detectable in the anomalous difference Fourier map. It is hoped that these improvements will lead towards XFEL experimental phase determination and structure determination by sulfur SAD and will generally increase the utility of the method for difficult cases.},
doi = {10.1107/S1399004715006902},
journal = {Acta Crystallographica. Section D: Biological Crystallography},
number = Pt 6,
place = {Denmark},
DOI: 10.1107/S1399004715006902
A revised partiality model and post-refinement algorithm for X-ray free-electron laser data
Journal Article Ginn, Helen Mary ; Brewster, Aaron S. ; Hattne, Johan ; ... - Acta Crystallographica. Section D: Biological Crystallography (Online)
Research towards using X-ray free-electron laser (XFEL) data to solve structures using experimental phasing methods such as sulfur single-wavelength anomalous dispersion (SAD) has been hampered by shortcomings in the diffraction models for X-ray diffraction from FELs. Owing to errors in the orientation matrix and overly simple partiality models, researchers have required large numbers of images to converge to reliable estimates for the structure-factor amplitudes, which may not be feasible for all biological systems. Here, data for cytoplasmic polyhedrosis virus type 17 (CPV17) collected at 1.3 Å wavelength at the Linac Coherent Light Source (LCLS) are revisited. A previously published definitionmore » of a partiality model for reflections illuminated by self-amplified spontaneous emission (SASE) pulses is built upon, which defines a fraction between 0 and 1 based on the intersection of a reflection with a spread of Ewald spheres modelled by a super-Gaussian wavelength distribution in the X-ray beam. A method of post-refinement to refine the parameters of this model is suggested. This has generated a merged data set with an overall discrepancy (by calculating theR splitvalue) of 3.15% to 1.46 Å resolution from a 7225-image data set. The atomic numbers of C, N and O atoms in the structure are distinguishable in the electron-density map. There are 13 S atoms within the 237 residues of CPV17, excluding the initial disordered methionine. These only possess 0.42 anomalous scattering electrons each at 1.3 Å wavelength, but the 12 that have single predominant positions are easily detectable in the anomalous difference Fourier map. It is hoped that these improvements will lead towards XFEL experimental phase determination and structure determination by sulfur SAD and will generally increase the utility of the method for difficult cases.« less
Structure of the Archaeoglobus fulgidus orphan ORF AF1382 determined by sulfur SAD from a moderately diffracting crystal
Journal Article Zhu, Jin-Yi ; Fu, Zheng-Qing ; Argonne National Laboratory, Argonne, Illinois ; ... - Acta Crystallographica. Section D: Biological Crystallography
The crystal structure of the 11.14 kDa orphan ORF 1382 from Archaeoglobus fulgidus (AF1382) has been determined by sulfur SAD phasing using data collected from a moderately diffracting crystal and 1.9 Å synchrotron X-rays. The crystal structure of the 11.14 kDa orphan ORF 1382 from Archaeoglobus fulgidus (AF1382) has been determined by sulfur SAD phasing using a moderately diffracting crystal and 1.9 Å wavelength synchrotron X-rays. AF1382 was selected as a structural genomics target by the Southeast Collaboratory for Structural Genomics (SECSG) since sequence analyses showed that it did not belong to the Pfam-A database and thus could represent amore » novel fold. The structure was determined by exploiting longer wavelength X-rays and data redundancy to increase the anomalous signal in the data. AF1382 is a 95-residue protein containing five S atoms associated with four methionine residues and a single cysteine residue that yields a calculated Bijvoet ratio (ΔF{sub anom}/F) of 1.39% for 1.9 Å wavelength X-rays. Coupled with an average Bijvoet redundancy of 25 (two 360° data sets), this produced an excellent electron-density map that allowed 69 of the 95 residues to be automatically fitted. The S-SAD model was then manually completed and refined (R = 23.2%, R{sub free} = 26.8%) to 2.3 Å resolution. High-resolution data were subsequently collected from a better diffracting crystal using 0.97 Å wavelength synchrotron X-rays and the S-SAD model was refined (R = 17.9%, R{sub free} = 21.4%) to 1.85 Å resolution. AF1382 has a winged-helix–turn–helix structure common to many DNA-binding proteins and most closely resembles the N-terminal domain (residues 1–82) of the Rio2 kinase from A. fulgidus, which has been shown to bind DNA, and a number of MarR-family transcriptional regulators, suggesting a similar DNA-binding function for AF1382. The analysis also points out the advantage gained from carrying out data reduction and structure determination on-site while the crystal is still available for further data collection.« less
Robust structural analysis of native biological macromolecules from multi-crystal anomalous diffraction data
Journal Article Liu, Qun ; Liu, Qinglian ; Hendrickson, Wayne A., E-mail: wayne@xtl.cumc.columbia.edu ; ... - Acta Crystallographica. Section D: Biological Crystallography
Anomalous diffraction signals from typical native macromolecules are very weak, frustrating their use in structure determination. Here, native SAD procedures are described for enhancing the signal to noise in anomalous diffraction by using multiple crystals are described. Five applications demonstrate that truly routine structure determination is possible without the need for heavy atoms. Structure determinations for biological macromolecules that have no known structural antecedents typically involve the incorporation of heavier atoms than those found natively in biological molecules. Currently, selenomethionyl proteins analyzed using single- or multi-wavelength anomalous diffraction (SAD or MAD) data predominate for such de novo analyses. Naturally occurringmore » metal ions such as zinc or iron often suffice in MAD or SAD experiments, and sulfur SAD has been an option since it was first demonstrated using crambin 30 years ago; however, SAD analyses of structures containing only light atoms (Z{sub max} ≤ 20) have not been common. Here, robust procedures for enhancing the signal to noise in measurements of anomalous diffraction by combining data collected from several crystals at a lower than usual X-ray energy are described. This multi-crystal native SAD method was applied in five structure determinations, using between five and 13 crystals to determine substructures of between four and 52 anomalous scatterers (Z ≤ 20) and then the full structures ranging from 127 to 1200 ordered residues per asymmetric unit at resolutions from 2.3 to 2.8 Å. Tests were devised to assure that all of the crystals used were statistically equivalent. Elemental identities for Ca, Cl, S, P and Mg were proven by f′′ scattering-factor refinements. The procedures are robust, indicating that truly routine structure determination of typical native macromolecules is realised. Synchrotron beamlines that are optimized for low-energy X-ray diffraction measurements will facilitate such direct structural analysis.« less
The hidden treasure in your data: phasing with unexpected weak anomalous scatterers from routine data sets
Journal Article Hegde, Raghurama P. ; Fedorov, Alexander A. ; Sauder, J. Michael ; ... - Acta Crystallographica. Section F, Structural Biology Communications
Single-wavelength anomalous dispersion (SAD) utilizing anomalous signal from native S atoms, or other atoms withZ≤ 20, generally requires highly redundant data collected using relatively long-wavelength X-rays. Here, the results from two proteins are presented where the anomalous signal from serendipitously acquired surface-bound Ca atoms with an anomalous data multiplicity of around 10 was utilized to drivede novostructure determination. In both cases, the Ca atoms were acquired from the crystallization solution, and the data-collection strategy was not optimized to exploit the anomalous signal from these scatterers. The X-ray data were collected at 0.98 Å wavelength in one case and at 1.74more » Å in the other (the wavelength was optimized for sulfur, but the anomalous signal from calcium was exploited for structure solution). Similarly, using a test case, it is shown that data collected at ~1.0 Å wavelength, where thef'' value for sulfur is 0.28 e, are sufficient for structure determination using intrinsic S atoms from a strongly diffracting crystal. Interestingly, it was also observed thatSHELXDwas capable of generating a substructure solution from high-exposure data with a completeness of 70% for low-resolution reflections extending to 3.5 Å resolution with relatively low anomalous multiplicity. Considering the fact that many crystallization conditions contain anomalous scatterers such as Cl, Ca, Mnetc., checking for the presence of fortuitous anomalous signal in data from well diffracting crystals could prove useful in either determining the structurede novoor in accurately assigning surface-bound atoms.« less
DOI: 10.1107/S2053230X17002680
Challenges of sulfur SAD phasing as a routine method in macromolecular crystallography
Journal Article Doutch, James ; Hough, Michael A. ; Hasnain, S. Samar ; ... - Journal of Synchrotron Radiation
The sulfur SAD phasing method allows the determination of protein structuresde novowithout reference to derivatives such as Se-methionine. The feasibility for routine automated sulfur SAD phasing using a number of current protein crystallography beamlines at several synchrotrons was examined using crystals of trimericAchromobacter cycloclastesnitrite reductase (AcNiR), which contains a near average proportion of sulfur-containing residues and two Cu atoms per subunit. Experiments using X-ray wavelengths in the range 1.9–2.4 Å show that we are not yet at the level where sulfur SAD is routinely successful forautomatedstructure solution and model building using existing beamlines and current software tools. On the othermore » hand, experiments using the shortest X-ray wavelengths available on existing beamlines could be routinely exploited to solve and produce unbiased structural models using the similarly weak anomalous scattering signals from the intrinsic metal atoms in proteins. The comparison of long-wavelength phasing (the Bijvoet ratio for nine S atoms and two Cu atoms is ~1.25% at ~2 Å) and copper phasing (the Bijvoet ratio for two Cu atoms is 0.81% at ~0.75Å) forAcNiR suggests that lower data multiplicity than is currently required for success should in general be possible for sulfur phasing if appropriate improvements to beamlines and data collection strategies can be implemented.« less