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Yorodumi- PDB-5hl4: Acoustic injectors for drop-on-demand serial femtosecond crystall... -
+Open data
-Basic information
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5hl4.cif.gz | 96.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5hl4.ent.gz | 72.5 KB | Display | PDB format |
PDBx/mmJSON format | 5hl4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hl/5hl4 ftp://data.pdbj.org/pub/pdb/validation_reports/hl/5hl4 | HTTPS FTP |
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-Related structure data
Related structure data | 5f81C 5hqdC 3vcpS 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: 46425.457 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sinorhizobium meliloti 1021 (bacteria) / Strain: 1021 / Gene: SMa0751 / Production host: Sinorhizobium meliloti 1021 (bacteria) / References: UniProt: Q92ZP9 |
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#2: Chemical | ChemComp-FES / |
#3: Chemical | ChemComp-FE / |
#4: Chemical | ChemComp-NCO / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.71 Å3/Da / Density % sol: 54.65 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 10 mg/ml protein with 25 mM hexaamine cobalt chloride crystallized by hanging drop with precipitant 7.5% PEG 3350, 10% glycerol, and 0.1M HEPES pH 7.0. |
-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: 2.2→90.04 Å / Num. obs: 25584 / % possible obs: 99.66 % / Redundancy: 53.6 % / Net I/σ(I): 16.5 |
Reflection shell | Resolution: 2.2→2.29 Å / Redundancy: 10.1 % / Mean I/σ(I) obs: 3.7 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3vcp Resolution: 2.2→90.04 Å / Cor.coef. Fo:Fc: 0.85 / Cor.coef. Fo:Fc free: 0.756 / SU B: 11.033 / SU ML: 0.266 / Cross valid method: THROUGHOUT / ESU R: 0.311 / ESU R Free: 0.266 / 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: 25.081 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→90.04 Å
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Refine LS restraints |
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