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Open data
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Basic information
Entry | Database: PDB / ID: 6cla | ||||||
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Title | 2.80 A MicroED structure of proteinase K at 6.0 e- / A^2 | ||||||
![]() | Proteinase K | ||||||
![]() | HYDROLASE | ||||||
Function / homology | ![]() peptidase K / serine-type endopeptidase activity / proteolysis / extracellular space / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ELECTRON CRYSTALLOGRAPHY / electron crystallography / ![]() | ||||||
![]() | Hattne, J. / Shi, D. / Glynn, C. / Zee, C.-T. / Gallagher-Jones, M. / Martynowycz, M.W. / Rodriguez, J.A. / Gonen, T. | ||||||
![]() | ![]() Title: Analysis of Global and Site-Specific Radiation Damage in Cryo-EM. Authors: Johan Hattne / Dan Shi / Calina Glynn / Chih-Te Zee / Marcus Gallagher-Jones / Michael W Martynowycz / Jose A Rodriguez / Tamir Gonen / ![]() Abstract: Micro-crystal electron diffraction (MicroED) combines the efficiency of electron scattering with diffraction to allow structure determination from nano-sized crystalline samples in cryoelectron ...Micro-crystal electron diffraction (MicroED) combines the efficiency of electron scattering with diffraction to allow structure determination from nano-sized crystalline samples in cryoelectron microscopy (cryo-EM). It has been used to solve structures of a diverse set of biomolecules and materials, in some cases to sub-atomic resolution. However, little is known about the damaging effects of the electron beam on samples during such measurements. We assess global and site-specific damage from electron radiation on nanocrystals of proteinase K and of a prion hepta-peptide and find that the dynamics of electron-induced damage follow well-established trends observed in X-ray crystallography. Metal ions are perturbed, disulfide bonds are broken, and acidic side chains are decarboxylated while the diffracted intensities decay exponentially with increasing exposure. A better understanding of radiation damage in MicroED improves our assessment and processing of all types of cryo-EM data. | ||||||
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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 | ![]() | 65.4 KB | Display | ![]() |
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PDB format | ![]() | 45.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7493MC ![]() 7490C ![]() 7491C ![]() 7492C ![]() 7494C ![]() 7495C ![]() 7496C ![]() 7497C ![]() 7498C ![]() 7499C ![]() 7500C ![]() 7501C ![]() 7502C ![]() 7503C ![]() 7504C ![]() 7505C ![]() 7506C ![]() 7507C ![]() 7508C ![]() 7509C ![]() 7510C ![]() 7511C ![]() 7512C ![]() 6cl7SC ![]() 6cl8C ![]() 6cl9C ![]() 6clbC ![]() 6clcC ![]() 6cldC ![]() 6cleC ![]() 6clfC ![]() 6clgC ![]() 6clhC ![]() 6cliC ![]() 6cljC ![]() 6clkC ![]() 6cllC ![]() 6clmC ![]() 6clnC ![]() 6cloC ![]() 6clpC ![]() 6clqC ![]() 6clrC ![]() 6clsC ![]() 6cltC |
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Similar structure data |
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 28930.783 Da / Num. of mol.: 1 / Fragment: UNP residues 106-384 / Source method: isolated from a natural source / Source: (natural) ![]() |
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-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: Proteinase K / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: all / Source: NATURAL | |||||||||||||||
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Molecular weight | Value: 0.028888994 MDa / Experimental value: NO | |||||||||||||||
Source (natural) | Organism: ![]() | |||||||||||||||
Buffer solution | pH: 8 | |||||||||||||||
Buffer component |
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Specimen | Conc.: 25 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 30 % | |||||||||||||||
Crystal | Preparation: electron diffraction |
-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: 5.1 sec. / Electron dose: 0.0357 e/Å2 / Film or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Num. of diffraction images: 240 / Num. of grids imaged: 1 / Num. of real images: 240 |
Image scans | Sampling size: 31.2 µm / Width: 2048 / Height: 2048 |
EM diffraction | Camera length: 1200 mm |
EM diffraction shell | Resolution: 2.8→2.87 Å / Fourier space coverage: 88.21 % / Multiplicity: 5.8 / Num. of structure factors: 374 / Phase residual: 71.28 ° |
EM diffraction stats | Fourier space coverage: 88.4 % / High resolution: 2.8 Å / Num. of intensities measured: 30596 / Num. of structure factors: 5423 / Phase error: 62.59 ° / Phase residual: 62.59 ° / Phase error rejection criteria: 0 / Rmerge: 0.536 / Rsym: 0.536 |
Detector | Date: Mar 7, 2016 |
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Processing
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EM software |
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EM 3D crystal entity | ∠α: 90 ° / ∠β: 90 ° / ∠γ: 90 ° / A: 67.4502 Å / B: 67.4502 Å / C: 100.818 Å / Space group name: P43212 / Space group num: 96 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
CTF correction | Type: NONE | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.8 Å / Resolution method: DIFFRACTION PATTERN/LAYERLINES / Symmetry type: 3D CRYSTAL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | B value: 29.658 / Protocol: OTHER / Space: RECIPROCAL / Details: Electron scattering factors | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 5I9S Pdb chain-ID: A / Accession code: 5I9S / Pdb chain residue range: 1-279 / Source name: PDB / Type: experimental model | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | Method to determine structure: ![]() Starting model: PDB entry 6CL7 Resolution: 2.8→50.01 Å / Cor.coef. Fo:Fc: 0.875 / Cor.coef. Fo:Fc free: 0.773 / SU B: 38.53 / SU ML: 0.79 / Cross valid method: THROUGHOUT / ESU R Free: 0.618 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.658 Å2
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Refinement step | Cycle: 1 / Total: 2029 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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