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Open data
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Basic information
Entry | Database: PDB / ID: 4r6f | ||||||
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Title | Crystal structure of computational designed protein DLRR_I | ||||||
![]() | Leucine rich repeat DLRR_I | ||||||
![]() | DE NOVO PROTEIN / Leucine rich motifs | ||||||
Function / homology | Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Alpha-Beta Horseshoe / Alpha Beta![]() | ||||||
Biological species | synthetic construct (others) | ||||||
Method | ![]() ![]() | ||||||
![]() | Shen, B.W. / Stoddard, B.L. | ||||||
![]() | ![]() Title: Control of repeat-protein curvature by computational protein design. Authors: Park, K. / Shen, B.W. / Parmeggiani, F. / Huang, P.S. / Stoddard, B.L. / Baker, D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 81.2 KB | Display | ![]() |
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PDB format | ![]() | 60.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 414 KB | Display | ![]() |
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Full document | ![]() | 416 KB | Display | |
Data in XML | ![]() | 15.6 KB | Display | |
Data in CIF | ![]() | 23.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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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: 36529.043 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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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41.47 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 24% PEG 3350, 0.1 M HEPES, 0.2 M Ammonium Sulfate, 0.1 M Proline, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||
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Diffraction source | Source: ![]() | ||||||||||||||||||||||||
Detector | Type: RIGAKU SATURN 70 / Detector: CCD / Date: Apr 15, 2014 / Details: mirrors | ||||||||||||||||||||||||
Radiation | Monochromator: Si (220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 1.73→66.1 Å / Num. all: 32346 / Num. obs: 31150 / % possible obs: 96.3 % / Observed criterion σ(I): 1 / Redundancy: 10.3 % / Rsym value: 0.076 / Net I/σ(I): 33.7 | ||||||||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: Computational designed template Resolution: 1.73→66.1 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.941 / SU B: 2.129 / SU ML: 0.07 / Cross valid method: THROUGHOUT / ESU R: 0.113 / ESU R Free: 0.115 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.703 Å2
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Refinement step | Cycle: LAST / Resolution: 1.73→66.1 Å
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Refine LS restraints |
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