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Yorodumi- PDB-6vhc: 1.4A damaged structure of GSNQNNF used to determine initial phase... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6vhc | ||||||
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Title | 1.4A damaged structure of GSNQNNF used to determine initial phases from radiation damage | ||||||
Components | GSNQNNF | ||||||
Keywords | PROTEIN FIBRIL / MicroED / damage / phasing / RIP | ||||||
Function / homology | ACETATE ION Function and homology information | ||||||
Biological species | synthetic construct (others) | ||||||
Method | ELECTRON CRYSTALLOGRAPHY / electron crystallography / cryo EM / Resolution: 1.4 Å | ||||||
Authors | Martynowycz, M.W. / Hattne, J. / Gonen, T. | ||||||
Citation | Journal: Structure / Year: 2020 Title: Experimental Phasing of MicroED Data Using Radiation Damage. Authors: Michael W Martynowycz / Johan Hattne / Tamir Gonen / Abstract: We previously demonstrated that microcrystal electron diffraction (MicroED) can be used to determine atomic-resolution structures from vanishingly small three-dimensional crystals. Here, we present ...We previously demonstrated that microcrystal electron diffraction (MicroED) can be used to determine atomic-resolution structures from vanishingly small three-dimensional crystals. Here, we present an example of an experimentally phased structure using only MicroED data. The structure of a seven-residue peptide is solved starting from differences to the diffraction intensities induced by structural changes due to radiation damage. The same wedge of reciprocal space was recorded twice by continuous-rotation MicroED from a set of 11 individual crystals. The data from the first pass were merged to make a "low-dose dataset." The data from the second pass were similarly merged to form a "damaged dataset." Differences between these two datasets were used to identify a single heavy-atom site from a Patterson difference map, and initial phases were generated. Finally, the structure was completed by iterative cycles of modeling and refinement. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6vhc.cif.gz | 12.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6vhc.ent.gz | 4.6 KB | Display | PDB format |
PDBx/mmJSON format | 6vhc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vh/6vhc ftp://data.pdbj.org/pub/pdb/validation_reports/vh/6vhc | HTTPS FTP |
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-Related structure data
Related structure data | 21203MC 6vhbC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein/peptide | Mass: 779.756 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-ACT / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: ELECTRON CRYSTALLOGRAPHY |
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EM experiment | Aggregation state: 3D ARRAY / 3D reconstruction method: electron crystallography |
-Sample preparation
Component | Name: Synthetic proto-filament / Type: COMPLEX / Entity ID: #1 / Source: NATURAL | |||||||||||||||
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Molecular weight | Value: 0.000899141 MDa / Experimental value: NO | |||||||||||||||
Source (natural) | Organism: synthetic construct (others) | |||||||||||||||
Buffer solution | pH: 6 | |||||||||||||||
Buffer component |
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Specimen | Conc.: 10 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: Hanging drop. | |||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/4 | |||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 30 % |
-Data collection
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Microscopy | Model: FEI TECNAI F20 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Electron lens | Mode: DIFFRACTION / C2 aperture diameter: 100 µm | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Specimen holder | Cryogen: NITROGEN Specimen holder model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Image recording | Average exposure time: 2.1 sec. / Electron dose: 0.00588 e/Å2 / Film or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Num. of diffraction images: 736 / Num. of grids imaged: 1 / Num. of real images: 736 / Details: Images collected as a movies. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Image scans | Sampling size: 31.2 µm / Width: 2048 / Height: 2048 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
EM diffraction | Camera length: 730 mm | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
EM diffraction shell | Resolution: 1.4→13.97 Å / Fourier space coverage: 78.1 % / Multiplicity: 8.7 / Num. of structure factors: 722 / Phase residual: 26 ° | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
EM diffraction stats | Details: Model from the low-dose set refined against the damage dataset without any changes. Fourier space coverage: 78.1 % / High resolution: 1.4 Å / Num. of intensities measured: 6314 / Num. of structure factors: 722 / Phase error: 26 ° / Phase residual: 26 ° / Phase error rejection criteria: 0 / Rmerge: 0.199 / Rsym: 0.21 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Highest resolution: 1.4 Å / Num. obs: 722 / % possible obs: 78.1 % / Redundancy: 8.745 % / Biso Wilson estimate: 10.108 Å2 / CC1/2: 0.982 / Rmerge(I) obs: 0.199 / Rrim(I) all: 0.21 / Χ2: 0.921 / Net I/σ(I): 8.67 / Num. measured all: 6314 / Scaling rejects: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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EM software | Name: EM-Menu / Version: 4.0.9.75 / Category: image acquisition | ||||||||||||||||||||
Image processing | Details: Rolling shutter and binned by 2. | ||||||||||||||||||||
EM 3D crystal entity | ∠α: 83.7 ° / ∠β: 85.43 ° / ∠γ: 82.96 ° / A: 4.85 Å / B: 14.15 Å / C: 17.43 Å / Space group name: 1 / Space group num: 1 | ||||||||||||||||||||
CTF correction | Type: NONE | ||||||||||||||||||||
3D reconstruction | Resolution method: DIFFRACTION PATTERN/LAYERLINES / Symmetry type: 3D CRYSTAL | ||||||||||||||||||||
Atomic model building | B value: 5 / Protocol: OTHER / Space: RECIPROCAL | ||||||||||||||||||||
Atomic model building | PDB-ID: 6CLJ Pdb chain-ID: A / Accession code: 6CLJ / Pdb chain residue range: 1-7 / Source name: PDB / Type: experimental model | ||||||||||||||||||||
Refinement | Resolution: 1.4→13.97 Å / Cross valid method: THROUGHOUT
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Displacement parameters | Biso max: 18.27 Å2 / Biso mean: 4.5087 Å2 / Biso min: 0.08 Å2 |