+Open data
-Basic information
Entry | Database: PDB / ID: 6rli | ||||||
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Title | The structure of the self-assembled 3fPizza6-SH crystal | ||||||
Components | 3fPizza6-SH | ||||||
Keywords | DE NOVO PROTEIN / Pizza / beta-propeller / de novo / artificial protein | ||||||
Biological species | synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.15 Å | ||||||
Authors | Noguchi, H. / Voet, A.R.D. | ||||||
Funding support | Belgium, 1items
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Citation | Journal: To Be Published Title: Self-assembled Pizza proteins Authors: Noguchi, H. / Voet, A.R.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6rli.cif.gz | 112.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6rli.ent.gz | 85.3 KB | Display | PDB format |
PDBx/mmJSON format | 6rli.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6rli_validation.pdf.gz | 418.6 KB | Display | wwPDB validaton report |
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Full document | 6rli_full_validation.pdf.gz | 421.8 KB | Display | |
Data in XML | 6rli_validation.xml.gz | 15.2 KB | Display | |
Data in CIF | 6rli_validation.cif.gz | 24.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rl/6rli ftp://data.pdbj.org/pub/pdb/validation_reports/rl/6rli | HTTPS FTP |
-Related structure data
Related structure data | 6rlhC 3ww9S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 25872.500 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli) |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.79 Å3/Da / Density % sol: 55.84 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion / Details: 20mM HEPES pH8 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 23, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.15→40.46 Å / Num. obs: 13784 / % possible obs: 87.8 % / Redundancy: 3.8 % / Biso Wilson estimate: 9.88 Å2 / Net I/σ(I): 10.6 |
Reflection shell | Resolution: 1.15→1.17 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 3.8 / Num. unique obs: 4510 / Rpim(I) all: 0.175 / % possible all: 93 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3ww9 Resolution: 1.15→40.46 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 22.92
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.15→40.46 Å
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Refine LS restraints |
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LS refinement shell |
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