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PDBsum entry 4zqx
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Viral protein
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PDB id
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4zqx
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PDB id:
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| Name: |
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Viral protein
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Title:
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A revised partiality model and post-refinement algorithm for x-ray free-electron laser data
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Structure:
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Polyhedrin. Chain: a. Engineered: yes
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Source:
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Uranotaenia sapphirina cypovirus. Organism_taxid: 311554. Expressed in: spodoptera frugiperda. Expression_system_taxid: 7108
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Resolution:
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1.46Å
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R-factor:
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0.110
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R-free:
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0.153
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Authors:
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H.M.Ginn,A.S.Brewster,J.Hattne,G.Evans,A.Wagner,J.Grimes,N.K.Sauter, G.Sutton,D.I.Stuart
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Key ref:
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H.M.Ginn
et al.
(2015).
A revised partiality model and post-refinement algorithm for X-ray free-electron laser data.
Acta Crystallogr D Biol Crystallogr,
71,
1400-1410.
PubMed id:
DOI:
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Date:
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11-May-15
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Release date:
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03-Jun-15
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PROCHECK
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Headers
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References
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Q5EK29
(Q5EK29_9REOV) -
Polyhedrin from Uranotaenia sapphirina cypovirus
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Seq:
Struc:
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237 a.a.
237 a.a.
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DOI no:
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Acta Crystallogr D Biol Crystallogr
71:1400-1410
(2015)
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PubMed id:
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A revised partiality model and post-refinement algorithm for X-ray free-electron laser data.
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H.M.Ginn,
A.S.Brewster,
J.Hattne,
G.Evans,
A.Wagner,
J.M.Grimes,
N.K.Sauter,
G.Sutton,
D.I.Stuart.
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ABSTRACT
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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
Rsplit 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.
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Links
