2-Phenylethyl 1-thio-β-<scp>D</scp>-galactopyranoside hemihydrate

Brito, Iván; Szilágyi, László; Kumar, Ambati Ashok; Albanez, Joselyn; Bolte, Michael

doi:10.1107/s1600536811031667

Cited by 2 publications

(1 citation statement)

References 8 publications

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“…For TRPV1 and β-galactosidase, non-crystallography symmetry (NCS) restraints were employed to account for rotational and dihedral symmetry. Reference restraints for PETG were obtained with phenix.elbow from the crystal structure of 2-phenylethyl 1-thio-β-D-galactopyranoside ( Brito et al, 2011 ). Building of glycans used glycan modeling tools available in Coot.…”

Section: Materials and Methodsmentioning

confidence: 99%

Model-based local density sharpening of cryo-EM maps

Jakobi

Wilmanns

Sachse

2017

eLife

229

219

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Atomic models based on high-resolution density maps are the ultimate result of the cryo-EM structure determination process. Here, we introduce a general procedure for local sharpening of cryo-EM density maps based on prior knowledge of an atomic reference structure. The procedure optimizes contrast of cryo-EM densities by amplitude scaling against the radially averaged local falloff estimated from a windowed reference model. By testing the procedure using six cryo-EM structures of TRPV1, β-galactosidase, γ-secretase, ribosome-EF-Tu complex, 20S proteasome and RNA polymerase III, we illustrate how local sharpening can increase interpretability of density maps in particular in cases of resolution variation and facilitates model building and atomic model refinement.

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Section: Materials and Methodsmentioning

confidence: 99%

Model-based local density sharpening of cryo-EM maps

Jakobi

Wilmanns

Sachse

2017

eLife

229

219

View full text Add to dashboard Cite

show abstract

Iterative model-based density improvement yields better atomic structures from cryo-EM maps

Jakobi

Wilmanns

Sachse

2017

Preprint

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16Atomic models based on high-resolution density maps are the ultimate result 17 of the cryo-EM structure determination process. Current cryo-EM model 18 refinement procedures work with the experimental density map that remains 19 constant throughout the process. Here, we introduce a general procedure that 20 iteratively improves cryo-EM density maps based on prior knowledge of an 21 atomic reference structure. The procedure optimizes contrast of cryo-EM 22 densities by local amplitude scaling (LocScale) based on an atomic model 23 without introducing model bias. We alternate the procedure with consecutive 24rounds of model refinement and tested it on four cryo-EM structures of 25 TRPV1, β-galactosidase, γ-secretase and RNA polymerase III. We 26 demonstrate that LocScale density improvement reveals previously 27 undiscovered map features and improves the quality of atomic models. The 28 presented approach enhances the interpretability of cryo-EM density maps 29 and provides an implementation reminiscent of iterative density improvement 30 as it is routinely employed in the refinement of X-ray crystallographic models.

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2-Phenylethyl 1-thio-β-D-galactopyranoside hemihydrate

Cited by 2 publications

References 8 publications

Model-based local density sharpening of cryo-EM maps

Model-based local density sharpening of cryo-EM maps

Iterative model-based density improvement yields better atomic structures from cryo-EM maps

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