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Yorodumi- PDB-5f81: Acoustic injectors for drop-on-demand serial femtosecond crystall... -
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-Basic information
Entry | Database: PDB / ID: 5f81 | ||||||||||||
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Title | Acoustic injectors for drop-on-demand serial femtosecond crystallography | ||||||||||||
Components | Lysozyme C | ||||||||||||
Keywords | HYDROLASE / LYSOZYME | ||||||||||||
Function / homology | Function and homology information Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium ...Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism / 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 / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 2.13 Å | ||||||||||||
Authors | Roessler, C.G. / Agarwal, R. / Allaire, M. / Alonso-Mori, R. / Andi, B. / Bachega, J.F.R. / Bommer, M. / Brewster, A.S. / Browne, M.C. / Chatterjee, R. ...Roessler, C.G. / Agarwal, R. / Allaire, M. / Alonso-Mori, R. / Andi, B. / Bachega, J.F.R. / Bommer, M. / Brewster, A.S. / Browne, M.C. / Chatterjee, R. / Cho, E. / Cohen, A.E. / Cowan, M. / Datwani, S. / Davidson, V.L. / Defever, J. / Eaton, B. / Ellson, R. / Feng, Y. / Ghislain, L.P. / Glownia, J.M. / Han, G. / Hattne, J. / Hellmich, J. / Heroux, A. / Ibrahim, M. / Kern, J. / Kuczewski, A. / Lemke, H.T. / Liu, P. / Majlof, L. / McClintock, W.M. / Myers, S. / Nelsen, S. / Olechno, J. / Orville, A.M. / Sauter, N.K. / Soares, A.S. / Soltis, M.S. / Song, H. / Stearns, R.G. / Tran, R. / Tsai, Y. / Uervirojnangkoorn, M. / Wilmot, C.M. / Yachandra, V. / Yano, J. / Yukl, E.T. / Zhu, D. / Zouni, A. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: Structure / Year: 2016 Title: Acoustic Injectors for Drop-On-Demand Serial Femtosecond Crystallography. Authors: Roessler, C.G. / Agarwal, R. / Allaire, M. / Alonso-Mori, R. / Andi, B. / Bachega, J.F. / Bommer, M. / Brewster, A.S. / Browne, M.C. / Chatterjee, R. / Cho, E. / Cohen, A.E. / Cowan, M. / ...Authors: Roessler, C.G. / Agarwal, R. / Allaire, M. / Alonso-Mori, R. / Andi, B. / Bachega, J.F. / Bommer, M. / Brewster, A.S. / Browne, M.C. / Chatterjee, R. / Cho, E. / Cohen, A.E. / Cowan, M. / Datwani, S. / Davidson, V.L. / Defever, J. / Eaton, B. / Ellson, R. / Feng, Y. / Ghislain, L.P. / Glownia, J.M. / Han, G. / Hattne, J. / Hellmich, J. / Heroux, A. / Ibrahim, M. / Kern, J. / Kuczewski, A. / Lemke, H.T. / Liu, P. / Majlof, L. / McClintock, W.M. / Myers, S. / Nelsen, S. / Olechno, J. / Orville, A.M. / Sauter, N.K. / Soares, A.S. / Soltis, S.M. / Song, H. / Stearns, R.G. / Tran, R. / Tsai, Y. / Uervirojnangkoorn, M. / Wilmot, C.M. / Yachandra, V. / Yano, J. / Yukl, E.T. / Zhu, D. / Zouni, A. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5f81.cif.gz | 43.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5f81.ent.gz | 29.4 KB | Display | PDB format |
PDBx/mmJSON format | 5f81.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5f81_validation.pdf.gz | 425.4 KB | Display | wwPDB validaton report |
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Full document | 5f81_full_validation.pdf.gz | 427.5 KB | Display | |
Data in XML | 5f81_validation.xml.gz | 9.3 KB | Display | |
Data in CIF | 5f81_validation.cif.gz | 12.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f8/5f81 ftp://data.pdbj.org/pub/pdb/validation_reports/f8/5f81 | HTTPS FTP |
-Related structure data
Related structure data | 5hl4C 5hqdC 4et8S 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 | ChemComp-NA / | ||
#3: Chemical | ChemComp-CL / #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.02 Å3/Da / Density % sol: 39.17 % |
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Crystal grow | Temperature: 295 K / Method: batch mode / pH: 4.6 Details: Batch crystallization 120 mg/ml dissolved in 0.1M sodium acetate (4.6), crystallized with 6% sodium chloride + 10% v/v glycerol |
-Data collection
Diffraction | Mean temperature: 295 K Ambient temp details: Acoustic specimen injection into xfel beam Serial crystal experiment: Y |
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Diffraction source | Source: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: XPP / Wavelength: 1.36 Å |
Detector | Type: CS-PAD XPP / Detector: PIXEL / Date: Jun 7, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.36 Å / Relative weight: 1 |
Reflection | Resolution: 2.13→55.51 Å / Num. obs: 6590 / % possible obs: 99.84 % / Redundancy: 15.6 % / Net I/σ(I): 14.7 |
Reflection shell | Resolution: 2.13→2.24 Å / Redundancy: 7.5 % / Mean I/σ(I) obs: 4.5 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4ET8 Resolution: 2.13→55.51 Å / Cor.coef. Fo:Fc: 0.868 / Cor.coef. Fo:Fc free: 0.744 / SU B: 11.066 / SU ML: 0.283 / Cross valid method: THROUGHOUT / ESU R: 0.406 / ESU R Free: 0.303 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.063 Å2
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Refinement step | Cycle: LAST / Resolution: 2.13→55.51 Å
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Refine LS restraints |
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