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- PDB-8ar9: Crystal to structure pipeline for ambient temperature, in situ cr... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8ar9 | ||||||
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Title | Crystal to structure pipeline for ambient temperature, in situ crystallography at beamline VMXi | ||||||
![]() | Nuclear receptor coactivator 7 | ||||||
![]() | ANTIVIRAL PROTEIN / NCOA7 / oxidative resistance | ||||||
Function / homology | ![]() : / negative regulation of cellular response to oxidative stress / negative regulation of peptidyl-cysteine S-nitrosylation / nuclear receptor coactivator activity / nuclear receptor binding / response to oxidative stress / regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleus Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Campeotto, I. / Foster, T. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Protein-to-structure pipeline for ambient-temperature in situ crystallography at VMXi. Authors: Mikolajek, H. / Sanchez-Weatherby, J. / Sandy, J. / Gildea, R.J. / Campeotto, I. / Cheruvara, H. / Clarke, J.D. / Foster, T. / Fujii, S. / Paulsen, I.T. / Shah, B.S. / Hough, M.A. #1: Journal: Acta Crystallogr.,Sect.D / Year: 2012 Title: Towards automated crystallographic structure refinement with phenix.refine. Authors: Afonine, P.V. / Grosse-Kunstleve, R.W. / Echols, N. / Headd, J.J. / Moriarty, N.W. / Mustyakimov, M. / Terwilliger, T.C. / Urzhumtsev, A. / Zwart, P.H. / Adams, P.D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 94.1 KB | Display | ![]() |
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PDB format | ![]() | 58.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 421.8 KB | Display | ![]() |
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Full document | ![]() | 423 KB | Display | |
Data in XML | ![]() | 8.4 KB | Display | |
Data in CIF | ![]() | 10.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7zckC ![]() 8a9dC ![]() 8ar6C ![]() 8brkC ![]() 8brlC ![]() 8cifC ![]() 4acjS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
#1: Protein | Mass: 20814.289 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.54 Å3/Da / Density % sol: 51.54 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 0.2 M di ammonium hydrogen citrate, 20% w/v PEG 3350 |
-Data collection
Diffraction | Mean temperature: 291 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 X 4M / Detector: PIXEL / Date: May 14, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.7749 Å / Relative weight: 1 |
Reflection | Resolution: 2.36→46.39 Å / Num. obs: 33925 / % possible obs: 92.55 % / Redundancy: 13.9 % / Biso Wilson estimate: 30.77 Å2 / CC1/2: 0.949 / Rmerge(I) obs: 0.483 / Rpim(I) all: 0.13 / Net I/σ(I): 5.7 |
Reflection shell | Resolution: 2.36→2.4 Å / Rmerge(I) obs: 2.335 / Num. unique obs: 420 / CC1/2: 0.261 / Rpim(I) all: 0.654 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4ACJ Resolution: 2.36→46.38 Å / SU ML: 0.3178 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.7765 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.35 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.36→46.38 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 20.2479846217 Å / Origin y: 16.1409668649 Å / Origin z: 9.95326992923 Å
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Refinement TLS group | Selection details: (chain A and resseq 21:183) |