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Yorodumi- PDB-7nje: gamma(S)-crystallin 9-site deamidation mutant grown inside HARE s... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7nje | ||||||
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Title | gamma(S)-crystallin 9-site deamidation mutant grown inside HARE serial crystallography chip | ||||||
Components | Gamma-crystallin S | ||||||
Keywords | STRUCTURAL PROTEIN / serial crystallography / crystallin / vapour diffusion / silicon chip | ||||||
Function / homology | Function and homology information structural constituent of eye lens / lens development in camera-type eye / visual perception / morphogenesis of an epithelium Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 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 | 7nje.cif.gz | 85.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7nje.ent.gz | 63.5 KB | Display | PDB format |
PDBx/mmJSON format | 7nje.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nj/7nje ftp://data.pdbj.org/pub/pdb/validation_reports/nj/7nje | HTTPS FTP |
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-Related structure data
Related structure data | 7njfC 7njgC 7njhC 7njiC 7njjC 7nkfC 6fd8S 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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-Components
#1: Protein | Mass: 20968.500 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CRYGS, CRYG8 / Production host: Escherichia coli (E. coli) / References: UniProt: P22914 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.88 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion Details: 50 mM HEPES pH 7.0, 20% PEG3350, 0.1 M sodium acetate pH 5.45 |
-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 R 4M / Detector: PIXEL / Date: Jun 27, 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: 3→69.6 Å / Num. obs: 8132 / % possible obs: 99.96 % / Redundancy: 48 % / Biso Wilson estimate: 52.32 Å2 / CC1/2: 0.9574 / Net I/σ(I): 2.5 |
Reflection shell | Resolution: 3→3.108 Å / Num. unique obs: 787 / CC1/2: 0.885 |
Serial crystallography sample delivery | Method: fixed target |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6FD8 Resolution: 3→69.6 Å / SU ML: 0.4305 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 41.481 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: 52.64 Å2 | ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→69.6 Å
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Refine LS restraints |
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Refine LS restraints NCS | Type: Torsion NCS / Rms dev position: 0.798069996017 Å | ||||||||||||||||||||||||||||
LS refinement shell |
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