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Yorodumi- PDB-6qxw: Pink beam serial crystallography: Lysozyme, 5 us exposure, 24344 ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6qxw | ||||||||||||||||||
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Title | Pink beam serial crystallography: Lysozyme, 5 us exposure, 24344 patterns merged (3 chips) | ||||||||||||||||||
Components | Lysozyme C | ||||||||||||||||||
Keywords | HYDROLASE / pink beam / fixed-target / serial crystallography / lysozyme | ||||||||||||||||||
Function / homology | Function and homology information Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / defense response to bacterium ...Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / defense response to bacterium / endoplasmic reticulum / extracellular space / identical protein binding / cytoplasm Similarity search - Function | ||||||||||||||||||
Biological species | Gallus gallus (chicken) | ||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||||||||||||||
Authors | Lieske, J. / Tolstikova, A. / Meents, A. | ||||||||||||||||||
Funding support | Germany, 5items
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Citation | Journal: Iucrj / Year: 2019 Title: 1 kHz fixed-target serial crystallography using a multilayer monochromator and an integrating pixel detector. Authors: Tolstikova, A. / Levantino, M. / Yefanov, O. / Hennicke, V. / Fischer, P. / Meyer, J. / Mozzanica, A. / Redford, S. / Crosas, E. / Opara, N.L. / Barthelmess, M. / Lieske, J. / Oberthuer, D. ...Authors: Tolstikova, A. / Levantino, M. / Yefanov, O. / Hennicke, V. / Fischer, P. / Meyer, J. / Mozzanica, A. / Redford, S. / Crosas, E. / Opara, N.L. / Barthelmess, M. / Lieske, J. / Oberthuer, D. / Wator, E. / Mohacsi, I. / Wulff, M. / Schmitt, B. / Chapman, H.N. / Meents, A. | ||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6qxw.cif.gz | 66.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6qxw.ent.gz | 48.7 KB | Display | PDB format |
PDBx/mmJSON format | 6qxw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qx/6qxw ftp://data.pdbj.org/pub/pdb/validation_reports/qx/6qxw | HTTPS FTP |
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-Related structure data
Related structure data | 6qxvC 6qxxC 6qxyC 6qy0C 6qy1C 6qy2C 6qy4C 6qy5C 6ftrS C: citing same article (ref.) 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: 14331.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: P00698, lysozyme | ||||||
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#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-EDO / | #5: 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: 2.11 Å3/Da / Density % sol: 41.84 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 3.5 Details: 50mM sodium acetate, 0.75M sodium chloride, 30% ethylene glycol, 11.25% polyethylene glycol 400 |
-Data collection
Diffraction | Mean temperature: 298 K / Serial crystal experiment: Y | |||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID09 / Wavelength: 0.8058-0.8262 | |||||||||
Detector | Type: PSI JUNGFRAU 1M / Detector: PIXEL / Date: Jul 15, 2017 | |||||||||
Radiation | Protocol: LAUE / Monochromatic (M) / Laue (L): L / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 1.7→28.235 Å / Num. obs: 14032 / % possible obs: 100 % / Redundancy: 315.5 % / CC1/2: 0.9894 / Net I/σ(I): 13.66 | |||||||||
Reflection shell | Resolution: 1.7→1.761 Å / CC1/2: 0.8439 | |||||||||
Serial crystallography sample delivery | Description: Roadrunner II / Method: fixed target | |||||||||
Serial crystallography sample delivery fixed target | Description: Roadrunner II |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6FTR Resolution: 1.7→28.235 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.87
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 93.36 Å2 / Biso mean: 25.0225 Å2 / Biso min: 8.66 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.7→28.235 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10 / % reflection obs: 100 %
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