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Open data
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Basic information
Entry | Database: PDB / ID: 5k7o | ||||||
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Title | MicroED structure of lysozyme at 1.8 A resolution | ||||||
![]() | Lysozyme C | ||||||
![]() | HYDROLASE | ||||||
Function / homology | ![]() Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium ...Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium / defense response to bacterium / endoplasmic reticulum / extracellular space / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ELECTRON CRYSTALLOGRAPHY / electron crystallography / cryo EM / Resolution: 1.8 Å | ||||||
![]() | de la Cruz, M.J. / Hattne, J. / Shi, D. / Seidler, P. / Rodriguez, J. / Reyes, F.E. / Sawaya, M.R. / Cascio, D. / Eisenberg, D. / Gonen, T. | ||||||
![]() | ![]() Title: Atomic-resolution structures from fragmented protein crystals with the cryoEM method MicroED. Authors: M Jason de la Cruz / Johan Hattne / Dan Shi / Paul Seidler / Jose Rodriguez / Francis E Reyes / Michael R Sawaya / Duilio Cascio / Simon C Weiss / Sun Kyung Kim / Cynthia S Hinck / Andrew P ...Authors: M Jason de la Cruz / Johan Hattne / Dan Shi / Paul Seidler / Jose Rodriguez / Francis E Reyes / Michael R Sawaya / Duilio Cascio / Simon C Weiss / Sun Kyung Kim / Cynthia S Hinck / Andrew P Hinck / Guillermo Calero / David Eisenberg / Tamir Gonen / ![]() Abstract: Traditionally, crystallographic analysis of macromolecules has depended on large, well-ordered crystals, which often require significant effort to obtain. Even sizable crystals sometimes suffer from ...Traditionally, crystallographic analysis of macromolecules has depended on large, well-ordered crystals, which often require significant effort to obtain. Even sizable crystals sometimes suffer from pathologies that render them inappropriate for high-resolution structure determination. Here we show that fragmentation of large, imperfect crystals into microcrystals or nanocrystals can provide a simple path for high-resolution structure determination by the cryoEM method MicroED and potentially by serial femtosecond crystallography. | ||||||
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 38 KB | Display | ![]() |
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PDB format | ![]() | 26.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 779 KB | Display | ![]() |
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Full document | ![]() | 778.5 KB | Display | |
Data in XML | ![]() | 7.5 KB | Display | |
Data in CIF | ![]() | 10.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8217MC ![]() 8216C ![]() 8218C ![]() 8219C ![]() 8220C ![]() 8221C ![]() 8222C ![]() 8472C ![]() 5k7nC ![]() 5k7pC ![]() 5k7qC ![]() 5k7rC ![]() 5k7sC ![]() 5k7tC ![]() 5ty4C M: map data used to model this data C: citing same article ( |
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Similar structure data | |
Experimental dataset #1 | Data reference: ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 14331.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() | ||||
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#2: Chemical | #3: Chemical | ChemComp-NA / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ELECTRON CRYSTALLOGRAPHY |
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EM experiment | Aggregation state: 3D ARRAY / 3D reconstruction method: electron crystallography |
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Sample preparation
Component | Name: Lysozyme / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1 / Source: NATURAL | |||||||||||||||
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Molecular weight | Value: 0.014386 MDa / Experimental value: NO | |||||||||||||||
Source (natural) | Organism: ![]() ![]() | |||||||||||||||
Buffer solution | pH: 4.7 | |||||||||||||||
Buffer component |
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Specimen | Conc.: 25 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||
Vitrification | Cryogen name: ETHANE |
-Data collection
Experimental equipment | ![]() Model: Tecnai F20 / Image courtesy: FEI Company | ||||||||||||||||||||||||
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Microscopy | Model: FEI TECNAI F20 | ||||||||||||||||||||||||
Electron gun | Electron source: ![]() | ||||||||||||||||||||||||
Electron lens | Mode: DIFFRACTION | ||||||||||||||||||||||||
Specimen holder | Cryogen: NITROGEN | ||||||||||||||||||||||||
Image recording | Average exposure time: 4.1 sec. / Electron dose: 0.004 e/Å2 / Film or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Num. of diffraction images: 1058 / Num. of grids imaged: 2 / Num. of real images: 1058 | ||||||||||||||||||||||||
Image scans | Sampling size: 0.0311999992 µm / Width: 2048 / Height: 2048 | ||||||||||||||||||||||||
EM diffraction | Camera length: 1500 mm | ||||||||||||||||||||||||
EM diffraction shell | Resolution: 1.8→2.06 Å / Fourier space coverage: 91.8 % / Multiplicity: 1.8 / Num. of structure factors: 3170 / Phase residual: 46.4 ° | ||||||||||||||||||||||||
EM diffraction stats | Fourier space coverage: 82.5 % / High resolution: 1.5 Å / Num. of intensities measured: 100693 / Num. of structure factors: 14955 / Phase error: 29.91 ° / Phase residual: 47.6 ° / Phase error rejection criteria: 0 / Rmerge: 0.618 / Rsym: 0.618 | ||||||||||||||||||||||||
Reflection | Resolution: 1.5→30.58 Å / Num. all: 100693 / Num. obs: 14955 / % possible obs: 82.5 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.618 / Rpim(I) all: 0.26 / Net I/σ(I): 2.7 | ||||||||||||||||||||||||
Reflection shell |
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Processing
Software | Name: PHENIX / Version: (1.10_2155: ???) / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||
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EM software |
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EM 3D crystal entity | ∠α: 90 ° / ∠β: 90 ° / ∠γ: 90 ° / A: 76.1 Å / B: 76.1 Å / C: 36.8 Å / Space group name: P43212 / Space group num: 96 | |||||||||||||||||||||||||||||||||||||||||||||
CTF correction | Type: NONE | |||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 1.8 Å / Resolution method: DIFFRACTION PATTERN/LAYERLINES / Symmetry type: 3D CRYSTAL | |||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: OTHER / Space: RECIPROCAL | |||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 3J6K Pdb chain-ID: A / Pdb chain residue range: 1-129 | |||||||||||||||||||||||||||||||||||||||||||||
Refinement | Resolution: 1.8→30.584 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.91
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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LS refinement shell |
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