+Open data
-Basic information
Entry | Database: PDB / ID: 7obf | ||||||
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Title | Crystal structure of the human VH antibody domain HEL4 | ||||||
Components | HEL4 | ||||||
Keywords | HYDROLASE / lysozyme / human VH antibody domain / HEL4 / immunoglobulin | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.699 Å | ||||||
Authors | Belviso, B.D. / Caliandro, R. / Carrozzini, B. | ||||||
Funding support | European Union, 1items
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Citation | Journal: To Be Published Title: Crystal structure of the human VH antibody domain HEL4 Authors: Belviso, B.D. / Caliandro, R. / Carrozzini, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7obf.cif.gz | 62.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7obf.ent.gz | 45.3 KB | Display | PDB format |
PDBx/mmJSON format | 7obf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7obf_validation.pdf.gz | 468.5 KB | Display | wwPDB validaton report |
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Full document | 7obf_full_validation.pdf.gz | 471.9 KB | Display | |
Data in XML | 7obf_validation.xml.gz | 13.2 KB | Display | |
Data in CIF | 7obf_validation.cif.gz | 17.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ob/7obf ftp://data.pdbj.org/pub/pdb/validation_reports/ob/7obf | HTTPS FTP |
-Related structure data
Related structure data | 1ohqS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Antibody | Mass: 13372.848 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) #2: Chemical | ChemComp-EPE / | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.58 Å3/Da / Density % sol: 52.36 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4 / Details: MgSO4, Hepes, glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.07234 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 23, 2018 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.07234 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.699→48.25 Å / Num. obs: 7840 / % possible obs: 99.1 % / Redundancy: 6.3 % / CC1/2: 0.968 / Rmerge(I) obs: 0.233 / Rpim(I) all: 0.099 / Rrim(I) all: 0.255 / Net I/σ(I): 8.1 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1ohq Resolution: 2.699→48.25 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 26.77 / Stereochemistry target values: ML
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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 max: 117.06 Å2 / Biso mean: 15.4485 Å2 / Biso min: 0.04 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.699→48.25 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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