- PDB-2j9v: 2 Angstrom X-ray structure of the yeast ESCRT-I Vps28 C-terminus -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 2j9v
Title
2 Angstrom X-ray structure of the yeast ESCRT-I Vps28 C-terminus
Components
VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 28Vacuole
Keywords
PROTEIN TRANSPORT / NZF FINGER / HIV BUDDING / VPS / MVB / CHMP / ESCRT / VPS36 / VPS28 / TRANSPORT
Function / homology
Function and homology information
ESCRT I complex / ATP export / Endosomal Sorting Complex Required For Transport (ESCRT) / protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / protein targeting to vacuole / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / protein targeting to membrane / late endosome membrane / endosome / protein-containing complex binding / cytosol Similarity search - Function
Monochromator: KHOZU / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.98 Å / Relative weight: 1
Reflection
Resolution: 2→64.28 Å / Num. obs: 10123 / % possible obs: 99.5 % / Observed criterion σ(I): 0 / Redundancy: 6.09 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 5.52
Reflection shell
Resolution: 2→2.11 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 1.81 / % possible all: 99.5
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Processing
Software
Name
Version
Classification
REFMAC
5.2.0019
refinement
MOSFLM
datareduction
SCALA
datascaling
PHASER
phasing
Refinement
Method to determine structure: MOLECULAR REPLACEMENT Starting model: SE DATASET FROM SEMET SUBSTITUTED CRYSTAL OF DIFFERENT CRYSTAL FORM Resolution: 2→42.22 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.922 / SU B: 4.53 / SU ML: 0.125 / Cross valid method: THROUGHOUT / ESU R: 0.175 / ESU R Free: 0.156 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.255
491
4.9 %
RANDOM
Rwork
0.228
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obs
0.229
9619
99.4 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK