+Open data
-Basic information
Entry | Database: PDB / ID: 7njj | ||||||
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Title | Proteinase K grown inside HARE serial crystallography chip | ||||||
Components | Proteinase K | ||||||
Keywords | HYDROLASE / serial crystallography / proteinase K / vapour diffusion / silicon chip | ||||||
Function / homology | Function and homology information peptidase K / serine-type endopeptidase activity / proteolysis / extracellular space / metal ion binding Similarity search - Function | ||||||
Biological species | Parengyodontium album (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | ||||||
Authors | Norton-Baker, B. / Mehrabi, P. / Boger, J. / Schonherr, R. / von Stetten, D. / Schikora, H. / Martin, R.W. / Miller, R.J.D. / Redecke, L. / Schulz, E.C. | ||||||
Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2021 Title: A simple vapor-diffusion method enables protein crystallization inside the HARE serial crystallography chip. Authors: Norton-Baker, B. / Mehrabi, P. / Boger, J. / Schonherr, R. / von Stetten, D. / Schikora, H. / Kwok, A.O. / Martin, R.W. / Miller, R.J.D. / Redecke, L. / Schulz, E.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7njj.cif.gz | 81.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7njj.ent.gz | 49.1 KB | Display | PDB format |
PDBx/mmJSON format | 7njj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nj/7njj ftp://data.pdbj.org/pub/pdb/validation_reports/nj/7njj | HTTPS FTP |
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-Related structure data
Related structure data | 7njeC 7njfC 7njgC 7njhC 7njiC 7nkfC 6j43S 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 28958.791 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Parengyodontium album (fungus) / References: UniProt: P06873, peptidase K |
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#2: Chemical | ChemComp-NO3 / |
#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: 2.2 Å3/Da / Density % sol: 44.16 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / Details: 1 M NaNO3, 0.1 M sodium citrate pH 6.5 |
-Data collection
Diffraction | Mean temperature: 293 K / Serial crystal experiment: Y |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9762 Å |
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jun 13, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→68.49 Å / Num. obs: 31851 / % possible obs: 100 % / Redundancy: 72 % / Biso Wilson estimate: 13.49 Å2 / CC1/2: 0.8986 / Net I/σ(I): 3.9 |
Reflection shell | Resolution: 1.65→1.709 Å / Num. unique obs: 3100 / CC1/2: 0.4112 |
Serial crystallography sample delivery | Method: fixed target |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6J43 Resolution: 1.65→57.95 Å / SU ML: 0.1663 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.9165 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 15.29 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.65→57.95 Å
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Refine LS restraints |
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LS refinement shell |
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