National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)
GM128867
United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)
P41GM136508
United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)
GM136614
United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)
GM007185
United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)
AI143368
United States
Sao Paulo Research Foundation (FAPESP)
16/24191-8
United States
Sao Paulo Research Foundation (FAPESP)
17/13485-3
Brazil
Spanish Ministry of Science, Innovation, and Universities
BES-2015-071397
United States
Spanish Ministry of Economy and Competitiveness
PGC2018-101370-B-100,
Spain
Spanish Ministry of Economy and Competitiveness
MDM2014-0435-01
Spain
Other government
2017SGR- 1192
Spain
Citation
Journal: ACS Bio Med Chem Au / Year: 2023 Title: Fragment-Based Phasing of Peptidic Nanocrystals by MicroED. Authors: Logan S Richards / Maria D Flores / Claudia Millán / Calina Glynn / Chih-Te Zee / Michael R Sawaya / Marcus Gallagher-Jones / Rafael J Borges / Isabel Usón / Jose A Rodriguez / Abstract: Electron diffraction (MicroED/3DED) can render the three-dimensional atomic structures of molecules from previously unamenable samples. The approach has been particularly transformative for peptidic ...Electron diffraction (MicroED/3DED) can render the three-dimensional atomic structures of molecules from previously unamenable samples. The approach has been particularly transformative for peptidic structures, where MicroED has revealed novel structures of naturally occurring peptides, synthetic protein fragments, and peptide-based natural products. Despite its transformative potential, MicroED is beholden to the crystallographic phase problem, which challenges its determination of structures. ARCIMBOLDO, an automated, fragment-based approach to structure determination, eliminates the need for atomic resolution, instead enforcing stereochemical constraints through libraries of small model fragments, and discerning congruent motifs in solution space to ensure validation. This approach expands the reach of MicroED to presently inaccessible peptide structures including fragments of human amyloids, and yeast and mammalian prions. For electron diffraction, fragment-based phasing portends a more general phasing solution with limited model bias for a wider set of chemical structures.
Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O
-
Experimental details
-
Experiment
Experiment
Method: ELECTRON CRYSTALLOGRAPHY
EM experiment
Aggregation state: 3D ARRAY / 3D reconstruction method: electron crystallography
-
Sample preparation
Component
Name: steric zipper structure of sequence variant of repeat segment of the yeast prion New1p Type: COMPLEX / Entity ID: #1 / Source: MULTIPLE SOURCES
Buffer solution
pH: 4.5
Specimen
Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Vitrification
Cryogen name: ETHANE
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Data collection
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
Microscopy
Model: FEI TALOS ARCTICA
Electron gun
Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lens
Mode: DIFFRACTION
Image recording
Electron dose: 0.05 e/Å2 / Film or detector model: TVIPS TEMCAM-F416 (4k x 4k)
EM diffraction
Camera length: 1000 mm
EM diffraction shell
Resolution (Å)
ID
EM diffraction stats-ID
Fourier space coverage (%)
Multiplicity
Num. of structure factors
Phase residual (°)
13.6007-2.7958
1
1
84
8.1
84
0.01
2.7958-2.2222
2
1
88
8.08
88
0.01
2.2222-1.9422
3
1
93
6.87
93
0.01
1.9422-1.7651
4
1
87
8.32
87
0.01
1.7651-1.6388
5
1
78
8.06
78
0.01
1.6388-1.5423
6
1
93
7.34
93
0.01
1.5423-1.4652
7
1
96
8.09
96
0.01
1.4652-1.4014
8
1
90
8.12
90
0.01
1.4014-1.3475
9
1
84
5.78
84
0.01
1.3475-1.3011
10
1
79
4.07
79
0.01
EM diffraction stats
Details: Phase error and phase residual statistics are not routinely reported for crystallographic structures. No imaging was used. The phases were obtained by an ab initio crystallographic method ...Details: Phase error and phase residual statistics are not routinely reported for crystallographic structures. No imaging was used. The phases were obtained by an ab initio crystallographic method described in our manuscript Fourier space coverage: 83.4 % / High resolution: 1.1 Å / Num. of intensities measured: 7893 / Num. of structure factors: 1357 / Phase error: 20.8 ° / Phase residual: 0.01 ° / Phase error rejection criteria: 0 / Rmerge: 21.1 / Rsym: 21.1
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