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- PDB-5rzt: EPB41L3 PanDDA analysis group deposition -- Crystal Structure of ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5rzt | ||||||
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Title | EPB41L3 PanDDA analysis group deposition -- Crystal Structure of the FERM domain of human EPB41L3 in complex with Z763030030 | ||||||
![]() | Isoform 2 of Band 4.1-like protein 3 | ||||||
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Function / homology | ![]() protein localization to paranode region of axon / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Bradshaw, W.J. / Katis, V.L. / Newman, J.A. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Gileadi, O. | ||||||
![]() | ![]() Title: EPB41L3 PanDDA analysis group deposition Authors: Bradshaw, W.J. / Katis, V.L. / Newman, J.A. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Gileadi, O. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 77.1 KB | Display | ![]() |
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PDB format | ![]() | 56.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Group deposition
ID | G_1002181 (51 entries) |
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Title | EPB41L3 PanDDA analysis group deposition |
Type | changed state |
Description | The FERM domain of HUMAN EPB41L3 screened against the Enamine DSI-poised fragment library by X-ray Crystallography at the XChem facility of Diamond Light Source beamline I04-1 |
-Related structure data
Related structure data | ![]() 6ibeS 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: 33395.305 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() | ||||||
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#2: Chemical | ChemComp-WJA / | ||||||
#3: Chemical | ![]() #4: Chemical | ChemComp-EDO / ![]() #5: Water | ChemComp-HOH / | ![]() Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.83 % / Mosaicity: 0 ° |
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Crystal grow![]() | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 0.075M ammonium nitrate, 0.1M MES pH 6.0, 6.5% PEG 2000, 6.5% PEG 3350, 6.5% PEG 4000, 6.5% PEG 5000, 10% ethylene glycol |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 2, 2019 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength![]() | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.79→49.71 Å / Num. obs: 28986 / % possible obs: 99.9 % / Redundancy: 6.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.038 / Rrim(I) all: 0.099 / Net I/σ(I): 12.3 / Num. measured all: 188150 / 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: 6IBE Resolution: 1.79→49.76 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.935 / SU B: 4.705 / SU ML: 0.135 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.188 / ESU R Free: 0.157 / 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: 88.88 Å2 / Biso mean: 36.214 Å2 / Biso min: 17.46 Å2
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Refinement step | Cycle: final / Resolution: 1.79→49.76 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.79→1.837 Å / Total num. of bins used: 20
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