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Open data
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Basic information
Entry | Database: PDB / ID: 7vty | ||||||
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Title | de novo designed protein | ||||||
![]() | de novo designed protein | ||||||
![]() | DE NOVO PROTEIN | ||||||
Biological species | synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zhang, L. | ||||||
Funding support | 1items
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![]() | ![]() Title: Rotamer-free protein sequence design based on deep learning and self-consistency. Authors: Zhang, L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 29.4 KB | Display | ![]() |
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PDB format | ![]() | 18.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7vqlC ![]() 7vqvC ![]() 7vqwC ![]() 7vu4C ![]() 1cy5S S: Starting model for refinement C: citing same article ( |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
#1: Protein | Mass: 10254.738 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.64 Å3/Da / Density % sol: 66.2 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 4% v/v Tacsimate pH 7.0 12% w/v Polyethylene glycol 3,350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Oct 4, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→48.27 Å / Num. obs: 4957 / % possible obs: 97 % / Redundancy: 6.1 % / Biso Wilson estimate: 68.52 Å2 / CC1/2: 0.997 / Net I/σ(I): 8.7 |
Reflection shell | Resolution: 2.5→2.6 Å / Num. unique obs: 569 / CC1/2: 0.766 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1cy5 Resolution: 2.5→39.62 Å / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 1.4 / Phase error: 22.46 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||
Displacement parameters | Biso max: 120.75 Å2 / Biso mean: 70.9146 Å2 / Biso min: 44.01 Å2 | |||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.5→39.62 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 2
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