+Open data
-Basic information
Entry | Database: PDB / ID: 7yiz | |||||||||
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Title | Crystal structure of anti-mPEG h15-2b Fab W104Y mutant | |||||||||
Components |
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Keywords | IMMUNE SYSTEM / methoxy polyethylene glycol / anti-mPEG antibody | |||||||||
Function / homology | 2,5,8,11,14,17-HEXAOXANONADECAN-19-OL Function and homology information | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.42 Å | |||||||||
Authors | Chang, C.Y. / Nguyen, T.M.T. / Li, Y.C. / Su, Y.C. | |||||||||
Funding support | Taiwan, 2items
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Citation | Journal: To Be Published Title: Crystal structure of anti-mPEG h15-2b Fab W104Y mutant Authors: Chang, C.Y. / Nguyen, T.M.T. / Li, Y.C. / Su, Y.C. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7yiz.cif.gz | 170.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7yiz.ent.gz | 137 KB | Display | PDB format |
PDBx/mmJSON format | 7yiz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7yiz_validation.pdf.gz | 882.2 KB | Display | wwPDB validaton report |
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Full document | 7yiz_full_validation.pdf.gz | 894.2 KB | Display | |
Data in XML | 7yiz_validation.xml.gz | 30.9 KB | Display | |
Data in CIF | 7yiz_validation.cif.gz | 43.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yi/7yiz ftp://data.pdbj.org/pub/pdb/validation_reports/yi/7yiz | HTTPS FTP |
-Related structure data
Related structure data | 7y0gS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Antibody | Mass: 23539.170 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster) #2: Antibody | Mass: 24575.320 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster) #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.91 Å3/Da / Density % sol: 57.72 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 18% (w/v) PEG-6000, 1% (w/v) PEG-2000-MME, 0.15 M lithium sulfate monohydrate, and 0.1 M citric acid |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 1 Å |
Detector | Type: RAYONIX MX300-HS / Detector: CCD / Date: Jun 12, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.42→30 Å / Num. obs: 42950 / % possible obs: 98.7 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 30.135 |
Reflection shell | Resolution: 2.42→2.51 Å / Redundancy: 6 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 3.7 / Num. unique obs: 3809 / % possible all: 89.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7Y0G Resolution: 2.42→29.81 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.881 / SU B: 8.562 / SU ML: 0.196 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.41 / ESU R Free: 0.285 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 106.52 Å2 / Biso mean: 37.099 Å2 / Biso min: 14.03 Å2
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Refinement step | Cycle: final / Resolution: 2.42→29.81 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.42→2.48 Å / Rfactor Rfree error: 0
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