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- PDB-5qsv: PanDDA analysis group deposition -- Crystal Structure of human ST... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5qsv | ||||||
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Title | PanDDA analysis group deposition -- Crystal Structure of human STAG1 in complex with Z2856434783 | ||||||
![]() | Cohesin subunit SA-1 | ||||||
![]() | TRANSCRIPTION / SGC - Diamond I04-1 fragment screening / PanDDA / XChemExplorer | ||||||
Function / homology | ![]() Cohesin Loading onto Chromatin / Establishment of Sister Chromatid Cohesion / cohesin complex / mitotic cohesin complex / establishment of mitotic sister chromatid cohesion / sister chromatid cohesion / mitotic spindle pole / chromosome, centromeric region / mitotic spindle assembly / SUMOylation of DNA damage response and repair proteins ...Cohesin Loading onto Chromatin / Establishment of Sister Chromatid Cohesion / cohesin complex / mitotic cohesin complex / establishment of mitotic sister chromatid cohesion / sister chromatid cohesion / mitotic spindle pole / chromosome, centromeric region / mitotic spindle assembly / SUMOylation of DNA damage response and repair proteins / Resolution of Sister Chromatid Cohesion / Meiotic synapsis / nuclear matrix / Separation of Sister Chromatids / chromosome / Estrogen-dependent gene expression / nuclear body / cell division / chromatin binding / chromatin / nucleoplasm / nucleus / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Newman, J.A. / Katis, V.L. / Gavard, A.E. / von Delft, F. / Arrowsmith, C.H. / Edwards, A. / Bountra, C. / Gileadi, O. | ||||||
![]() | ![]() Title: PanDDA analysis group deposition Authors: Newman, J.A. / Katis, V.L. / Gavard, A.E. / von Delft, F. / Arrowsmith, C.H. / Edwards, A. / 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 | ![]() | 260.3 KB | Display | ![]() |
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PDB format | ![]() | 210.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Group deposition
ID | G_1002084 (5 entries) |
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Title | PanDDA analysis group deposition |
Type | changed state |
Description | Human STAG1 site I screened against the 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 | ![]() 6qb5S 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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1 | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 39629.531 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-O3G / | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.14 Å3/Da / Density % sol: 60.81 % / Mosaicity: 0.14 ° |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.1 M Bis Tris Propane pH 7.0, 0.2 M Sodium Malonate, 20 % PEG 3350, 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: Jul 2, 2018 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.91587 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.76→60.64 Å / Num. obs: 47491 / % possible obs: 95.3 % / Redundancy: 1.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.041 / Rpim(I) all: 0.041 / Rrim(I) all: 0.058 / Net I/σ(I): 10.1 / Num. measured all: 85812 / 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: 6qb5 Resolution: 2.76→58.68 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.926 / SU B: 17.597 / SU ML: 0.323 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.83 / ESU R Free: 0.354 / 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: 221.21 Å2 / Biso mean: 95.044 Å2 / Biso min: 30 Å2
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Refinement step | Cycle: final / Resolution: 2.76→58.68 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.76→2.832 Å / Total num. of bins used: 20
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