- PDB-7bqi: Crystal structure of FYCO1 RUN domain -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 7bqi
Title
Crystal structure of FYCO1 RUN domain
Components
FYVE and coiled-coil domain-containing protein 1
Keywords
CYTOSOLIC PROTEIN / Autophagy
Function / homology
Function and homology information
plus-end-directed vesicle transport along microtubule / positive regulation of autophagosome maturation / autophagosome / late endosome / lysosome / intracellular membrane-bounded organelle / Golgi apparatus / membrane / metal ion binding Similarity search - Function
: / : / RUN domain / RUN domain superfamily / RUN domain / RUN domain profile. / GOLD domain superfamily / GOLD domain / GOLD domain profile. / FYVE zinc finger ...: / : / RUN domain / RUN domain superfamily / RUN domain / RUN domain profile. / GOLD domain superfamily / GOLD domain / GOLD domain profile. / FYVE zinc finger / FYVE zinc finger / Protein present in Fab1, YOTB, Vac1, and EEA1 / Zinc finger, FYVE-related / Zinc finger FYVE/FYVE-related type profile. / Zinc finger, FYVE/PHD-type / Zinc finger, RING/FYVE/PHD-type Similarity search - Domain/homology
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 1 Å / Relative weight: 1
Reflection
Resolution: 1.3→50 Å / Num. obs: 38506 / % possible obs: 90.7 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.092 / Net I/σ(I): 41.6
Reflection shell
Resolution: 1.3→1.32 Å / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 4.5 / Num. unique obs: 1885
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Processing
Software
Name
Version
Classification
REFMAC
5.8.0049
refinement
PDB_EXTRACT
3.25
dataextraction
HKL-2000
datareduction
HKL-2000
datascaling
AutoSol
phasing
Refinement
Method to determine structure: SIRAS Starting model: SAD model Resolution: 1.3→45.6 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.925 / SU B: 0.948 / SU ML: 0.041 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.067 / ESU R Free: 0.069 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.2399
1932
5 %
RANDOM
Rwork
0.2114
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obs
0.2129
36472
90.71 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
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