+Open data
-Basic information
Entry | Database: PDB / ID: 7njh | ||||||
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Title | HEX1 (in cellulo) grown inside HARE serial crystallography chip | ||||||
Components | Woronin body major protein | ||||||
Keywords | STRUCTURAL PROTEIN / serial crystallography / HEX1 / in-cellulo / silicon chip | ||||||
Function / homology | Function and homology information Woronin body / positive regulation of translational termination / positive regulation of translational elongation / cell septum / translational elongation / translation elongation factor activity / ribosome binding / RNA binding Similarity search - Function | ||||||
Biological species | Neurospora crassa (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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 | 7njh.cif.gz | 47.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7njh.ent.gz | 28.2 KB | Display | PDB format |
PDBx/mmJSON format | 7njh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7njh_validation.pdf.gz | 307.9 KB | Display | wwPDB validaton report |
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Full document | 7njh_full_validation.pdf.gz | 307.9 KB | Display | |
Data in XML | 7njh_validation.xml.gz | 7.4 KB | Display | |
Data in CIF | 7njh_validation.cif.gz | 9.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nj/7njh ftp://data.pdbj.org/pub/pdb/validation_reports/nj/7njh | HTTPS FTP |
-Related structure data
Related structure data | 7njeC 7njfC 7njgC 7njiC 7njjC 7nkfC 1khiS 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: 19150.664 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987) (fungus) Strain: ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987 Gene: hex-1, NCU08332 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P87252 |
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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: 2.49 Å3/Da / Density % sol: 50.59 % |
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Crystal grow | Temperature: 300 K / Method: in cell Details: Transfected and grown in Spodoptera frugiperda Sf9 insect cells |
-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: 2.5→64.1 Å / Num. obs: 7394 / % possible obs: 99.87 % / Redundancy: 37 % / Biso Wilson estimate: 51.89 Å2 / CC1/2: 0.8364 / Net I/σ(I): 3.1 |
Reflection shell | Resolution: 2.5→50.71 Å / Num. unique obs: 706 / CC1/2: 0.6878 |
Serial crystallography sample delivery | Method: fixed target |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1KHI Resolution: 2.5→50.71 Å / SU ML: 0.4002 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.1062 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: 55.55 Å2 | ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→50.71 Å
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Refine LS restraints |
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LS refinement shell |
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