+Open data
-Basic information
Entry | Database: PDB / ID: 7kqq | ||||||
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Title | Crystal structure of human WDR55 | ||||||
Components | WD repeat-containing protein 55 | ||||||
Keywords | NUCLEAR PROTEIN / WDR55 / WD-repeat / Structural Genomics Consortium / SGC | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Zeng, H. / Hutchinson, A. / Li, Y. / Seitova, A. / Edwards, A.M. / Arrowsmith, C.H. / Halabelian, L. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: To Be Published Title: Crystal structure of human WDR55 Authors: Zeng, H. / Hutchinson, A. / Li, Y. / Seitova, A. / Edwards, A.M. / Arrowsmith, C.H. / Halabelian, L. / Structural Genomics Consortium (SGC) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7kqq.cif.gz | 137.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7kqq.ent.gz | 105.1 KB | Display | PDB format |
PDBx/mmJSON format | 7kqq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kq/7kqq ftp://data.pdbj.org/pub/pdb/validation_reports/kq/7kqq | HTTPS FTP |
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-Related structure data
Related structure data | 1tbgS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 34350.836 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: WDR55 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9H6Y2 #2: Chemical | ChemComp-UNX / #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.96 Å3/Da / Density % sol: 58.42 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / Details: 20% W/V PEG 3350, 0.2 M Potassium Thiocyanate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97911 Å | |||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Aug 7, 2020 | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97911 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 1.8→48.75 Å / Num. obs: 72091 / % possible obs: 96.9 % / Redundancy: 3.2 % / CC1/2: 0.995 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.045 / Rrim(I) all: 0.085 / Net I/σ(I): 8.2 / Num. measured all: 234127 / Scaling rejects: 300 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Redundancy: 3.4 %
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1TBG Resolution: 1.8→48.75 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.943 / WRfactor Rfree: 0.2481 / WRfactor Rwork: 0.201 / FOM work R set: 0.823 / SU B: 2.902 / SU ML: 0.087 / SU R Cruickshank DPI: 0.1117 / SU Rfree: 0.1168 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.112 / ESU R Free: 0.117 / 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: 103.23 Å2 / Biso mean: 33.375 Å2 / Biso min: 4.63 Å2
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Refinement step | Cycle: final / Resolution: 1.8→48.75 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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