regulation of protein monoubiquitination / Signaling by cytosolic PDGFRA and PDGFRB fusion proteins / deubiquitinase activator activity / skeletal system morphogenesis / skin development / seminiferous tubule development / protein deubiquitination / positive regulation of double-strand break repair via homologous recombination / homeostasis of number of cells / single fertilization ...regulation of protein monoubiquitination / Signaling by cytosolic PDGFRA and PDGFRB fusion proteins / deubiquitinase activator activity / skeletal system morphogenesis / skin development / seminiferous tubule development / protein deubiquitination / positive regulation of double-strand break repair via homologous recombination / homeostasis of number of cells / single fertilization / embryonic organ development / ubiquitin binding / positive regulation of epithelial cell proliferation / Fanconi Anemia Pathway / Recognition of DNA damage by PCNA-containing replication complex / positive regulation of receptor signaling pathway via JAK-STAT / double-strand break repair via homologous recombination / multicellular organism growth / late endosome / single-stranded DNA binding / spermatogenesis / double-stranded DNA binding / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / lysosome / Ub-specific processing proteases / cysteine-type endopeptidase activity / intracellular membrane-bounded organelle / DNA damage response / proteolysis / DNA binding / nucleoplasm / nucleus / metal ion binding / plasma membrane / cytoplasm / cytosol Similarity search - Function
WDR48/Bun107 / Domain of unknown function (DUF3337) / Ubiquitin specific protease (USP) domain signature 2. / Ubiquitin specific protease (USP) domain signature 1. / Ubiquitin specific protease, conserved site / Peptidase C19, ubiquitin carboxyl-terminal hydrolase / Ubiquitin carboxyl-terminal hydrolase / Ubiquitin specific protease domain / Ubiquitin specific protease (USP) domain profile. / Papain-like cysteine peptidase superfamily ...WDR48/Bun107 / Domain of unknown function (DUF3337) / Ubiquitin specific protease (USP) domain signature 2. / Ubiquitin specific protease (USP) domain signature 1. / Ubiquitin specific protease, conserved site / Peptidase C19, ubiquitin carboxyl-terminal hydrolase / Ubiquitin carboxyl-terminal hydrolase / Ubiquitin specific protease domain / Ubiquitin specific protease (USP) domain profile. / Papain-like cysteine peptidase superfamily / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily Similarity search - Domain/homology
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 1.283 Å / Relative weight: 1
Reflection
Resolution: 3.3→50.01 Å / Num. obs: 16052 / % possible obs: 98.1 % / Redundancy: 8.4 % / Rmerge(I) obs: 0.102 / Rsym value: 0.109 / Net I/σ(I): 28.2
Reflection shell
Resolution: 3.3→3.36 Å / Redundancy: 6.1 % / % possible all: 96.4
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Processing
Software
Name
Version
Classification
REFMAC
5.8.0131
refinement
Coot
modelbuilding
PHENIX
phasing
HKL-2000
datareduction
HKL-2000
datascaling
Refinement
Method to determine structure: SAD / Resolution: 3.3→50.01 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.925 / Cross valid method: THROUGHOUT / ESU R Free: 0.607 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.28551
814
4.8 %
RANDOM
Rwork
0.23498
-
-
-
obs
0.23737
16052
97.95 %
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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