+Open data
-Basic information
Entry | Database: PDB / ID: 7lsi | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of KD035, a VEGFR2 monoclonal antibody | ||||||
Components |
| ||||||
Keywords | ANTITUMOR PROTEIN / IMMUNE SYSTEM / VEGFR2 / antibody | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Depetris, R.S. | ||||||
Citation | Journal: To Be Published Title: Structure of KD035, a VEGFR2 monoclonal antibody Authors: Depetris, R.S. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7lsi.cif.gz | 169.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7lsi.ent.gz | 133.3 KB | Display | PDB format |
PDBx/mmJSON format | 7lsi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7lsi_validation.pdf.gz | 446.3 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7lsi_full_validation.pdf.gz | 458.7 KB | Display | |
Data in XML | 7lsi_validation.xml.gz | 32.2 KB | Display | |
Data in CIF | 7lsi_validation.cif.gz | 45.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ls/7lsi ftp://data.pdbj.org/pub/pdb/validation_reports/ls/7lsi | HTTPS FTP |
-Related structure data
Related structure data | 3n9gS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Antibody | Mass: 23132.863 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) #2: Antibody | Mass: 22574.934 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 42.38 % |
---|---|
Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop Details: 0.2M Na Phosphate monobasic monohydrate,20% PEG3350 |
-Data collection
Diffraction | Mean temperature: 62 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 0.987 Å |
Detector | Type: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Feb 2, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 |
Reflection | Resolution: 1.99→39.46 Å / Num. obs: 50743 / % possible obs: 96.5 % / Redundancy: 3.3 % / CC1/2: 0.9 / Net I/σ(I): 6.7 |
Reflection shell | Resolution: 1.99→2.06 Å / Num. unique obs: 4626 / CC1/2: 0.31 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3N9G Resolution: 2.4→39.456 Å / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 30.53 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 72.5 Å2 / Biso mean: 33.9262 Å2 / Biso min: 13.74 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.4→39.456 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
|