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- PDB-5qqf: PanDDA analysis group deposition -- Crystal Structure of Kalirin/... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5qqf | ||||||
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Title | PanDDA analysis group deposition -- Crystal Structure of Kalirin/Rac1 in complex with MolPort-004-412-710 | ||||||
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![]() | Hydrolase/Transferase / SGC - Diamond I04-1 fragment screening / XChemExplorer / Hydrolase-Transferase complex | ||||||
Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Gray, J.L. / Krojer, T. / Talon, R. / Douangamath, A. / Jimenez Antunez, C. / Bountra, C. / Arrowsmith, C.H. / Edwards, A. / Brennan, P.E. / von Delft, F. | ||||||
![]() | ![]() Title: PanDDA analysis group deposition Authors: Gray, J.L. / Krojer, T. / Talon, R. / Douangamath, A. / Jimenez Antunez, C. / Bountra, C. / Arrowsmith, C.H. / Edwards, A. / Brennan, P.E. / von Delft, F. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 89 KB | Display | ![]() |
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PDB format | ![]() | 69.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 322.9 KB | Display | ![]() |
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Full document | ![]() | 324.3 KB | Display | |
Data in XML | ![]() | 19.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Group deposition
ID | G_1002072 (11 entries) |
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Title | PanDDA analysis group deposition |
Type | changed state |
Description | Kalirin/Rac1 complex screened against a customized urea fragment library by X-ray Crystallography at the XChem facility of Diamond Light Source beamline I04-1 |
-Related structure data
Related structure data | ![]() 5o33S S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 19797.844 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() |
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#2: Protein | ![]() Mass: 21274.471 Da / Num. of mol.: 1 / Mutation: None Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() References: UniProt: O60229, ![]() |
#3: Chemical | ChemComp-EDO / ![]() |
#4: Chemical | ChemComp-N5V / |
#5: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47.47 % / Mosaicity: 0.31 ° |
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Crystal grow![]() | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 0.1M bis-tris pH 5.5 24% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 3, 2018 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength![]() | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.26→54.12 Å / Num. obs: 19514 / % possible obs: 99.2 % / Redundancy: 10.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.137 / Rpim(I) all: 0.039 / Rrim(I) all: 0.143 / Net I/σ(I): 10.9 / Num. measured all: 208313 / Scaling rejects: 0 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing![]() | Method: ![]() |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 5O33 Resolution: 2.26→56.88 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.924 / SU B: 12.435 / SU ML: 0.268 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.336 / ESU R Free: 0.258 / 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: 134.83 Å2 / Biso mean: 52.975 Å2 / Biso min: 27.72 Å2
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Refinement step | Cycle: final / Resolution: 2.26→56.88 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.265→2.323 Å / Total num. of bins used: 20
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