+Open data
-Basic information
Entry | Database: PDB / ID: 6nek | ||||||
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Title | Crystal structure of a consensus PDZ domain | ||||||
Components | Consensus PDZ domain | ||||||
Keywords | DE NOVO PROTEIN / Consensus design / PDZ domain | ||||||
Biological species | synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.63 Å | ||||||
Authors | Sun, Y.J. / Gakhar, L. / Fuentes, E.J. | ||||||
Funding support | United States, 1items
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Citation | Journal: To be published Title: Consensus PDZ domain Authors: Sun, Y.J. / Sternke, M. / Barrick, D. / Fuentes, E.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6nek.cif.gz | 62.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6nek.ent.gz | 46.6 KB | Display | PDB format |
PDBx/mmJSON format | 6nek.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6nek_validation.pdf.gz | 428.9 KB | Display | wwPDB validaton report |
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Full document | 6nek_full_validation.pdf.gz | 428.9 KB | Display | |
Data in XML | 6nek_validation.xml.gz | 6.4 KB | Display | |
Data in CIF | 6nek_validation.cif.gz | 8.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ne/6nek ftp://data.pdbj.org/pub/pdb/validation_reports/ne/6nek | HTTPS FTP |
-Related structure data
Related structure data | 2w4fS S: Starting model for refinement |
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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 on special symmetry positions |
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-Components
#1: Protein | Mass: 9820.028 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: MET A1, GLY A2, TRP A3, GLY A85, GLY A86, GLY A87, HIS A88, HIS A89, HIS A90, HIS A91, HIS A92, HIS A93 are expression tags Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli) | ||
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#2: Chemical | #3: 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: 3.1 Å3/Da / Density % sol: 59.09 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.8 / Details: 0.5M LiSO4 2% w/v PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.0003 Å |
Detector | Type: RDI CMOS_8M / Detector: CMOS / Date: Mar 19, 2018 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0003 Å / Relative weight: 1 |
Reflection | Resolution: 1.63→46.49 Å / Num. obs: 15141 / % possible obs: 100 % / Redundancy: 2 % / CC1/2: 0.996 / Rmerge(I) obs: 0.016 / Rpim(I) all: 0.016 / Rrim(I) all: 0.023 / Net I/σ(I): 27.5 |
Reflection shell | Resolution: 1.63→1.69 Å / Redundancy: 2 % / Rmerge(I) obs: 0.471 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 1488 / CC1/2: 0.704 / Rpim(I) all: 0.471 / Rrim(I) all: 0.666 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2W4F Resolution: 1.63→46.47 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.47 / 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 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.63→46.47 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 1.1407 Å / Origin y: 26.3951 Å / Origin z: 12.0446 Å
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Refinement TLS group | Selection details: ALL |