+Open data
-Basic information
Entry | Database: PDB / ID: 3w9d | ||||||
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Title | Structure of Human Monoclonal Antibody E317 Fab | ||||||
Components |
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Keywords | IMMUNE SYSTEM / IgG fold / HSV gD | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta Function and homology information | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.32 Å | ||||||
Authors | Lee, C.C. / Lin, L.L. / Wang, A.H.J. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2013 Title: Structural basis for the antibody neutralization of herpes simplex virus Authors: Lee, C.C. / Lin, L.L. / Chan, W.E. / Ko, T.P. / Lai, J.S. / Wang, A.H.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3w9d.cif.gz | 176.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3w9d.ent.gz | 145.6 KB | Display | PDB format |
PDBx/mmJSON format | 3w9d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w9/3w9d ftp://data.pdbj.org/pub/pdb/validation_reports/w9/3w9d | HTTPS FTP |
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-Related structure data
-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: 23618.529 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pTCAE8 / Cell (production host): Mammalian cell / Cell line (production host): PER.C6 / Production host: Homo sapiens (human) #2: Antibody | Mass: 23133.602 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pTCAE8 / Cell (production host): Mammalian cell / Cell line (production host): PER.C6 / Production host: Homo sapiens (human) #3: Water | ChemComp-HOH / | |
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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: 2.54 Å3/Da / Density % sol: 51.63 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 5.8 Details: 25%(w/v) PEG 4000, 10mM calcium chloride dihydrate, 100mM sodium citrate tribasic dihydrate, pH 5.8, VAPOR DIFFUSION, temperature 298K |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Nov 20, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.32→30 Å / Num. all: 41992 / Num. obs: 40644 / % possible obs: 96.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 3.3 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 29.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.32→23 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.909 / SU B: 7.477 / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.366 / ESU R Free: 0.263 / 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: 32.413 Å2
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Refinement step | Cycle: LAST / Resolution: 2.32→23 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.316→2.376 Å / Total num. of bins used: 20
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