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- PDB-5qsn: 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: 5qsn | ||||||
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Title | PanDDA analysis group deposition -- Crystal Structure of human STAG1 in complex with Z1272480091 | ||||||
![]() | Cohesin subunit SA-1![]() | ||||||
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Function / homology | ![]() Cohesin Loading onto Chromatin / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() 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 | ![]() | 185.6 KB | Display | ![]() |
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PDB format | ![]() | 147.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Group deposition
ID | G_1002083 (7 entries) |
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Title | PanDDA analysis group deposition |
Type | changed state |
Description | Human STAG1 site IV 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 | ![]() 6r7oS 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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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | ![]() Mass: 52752.941 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-O2J / ( | #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: 2.9 Å3/Da / Density % sol: 57.6 % / Mosaicity: 0 ° |
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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: Apr 13, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.66→113.82 Å / Num. obs: 36436 / % possible obs: 100 % / Redundancy: 6.3 % / CC1/2: 0.997 / Rmerge(I) obs: 0.13 / Rpim(I) all: 0.061 / Rrim(I) all: 0.154 / Net I/σ(I): 7 / Num. measured all: 229809 / Scaling rejects: 2 |
Reflection shell | Resolution: 2.66→2.73 Å / % possible obs: 100 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.86 / Mean I/σ(I) all: 1.3 / Mean I/σ(I) obs: 1.3 / Num. measured obs: 15843 / Num. unique obs: 2602 / CC1/2: 0.365 / Rpim(I) all: 0.433 / Rrim(I) all: 0.1073 / % possible all: 100 |
-Phasing
Phasing![]() | Method: ![]() |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 6r7o Resolution: 2.66→113.82 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.931 / SU B: 21.796 / SU ML: 0.392 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.631 / ESU R Free: 0.353 / 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: 193.13 Å2 / Biso mean: 75.092 Å2 / Biso min: 39.85 Å2
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Refinement step | Cycle: final / Resolution: 2.66→113.82 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.657→2.726 Å / Total num. of bins used: 20
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