- PDB-5uki: Mn2+ and Zn2+ requirements for the lariat debranching enzyme, Dbr1 -
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ID or keywords:
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Basic information
Entry
Database: PDB / ID: 5uki
Title
Mn2+ and Zn2+ requirements for the lariat debranching enzyme, Dbr1
Components
RNA lariat debranching enzyme, putative
Keywords
HYDROLASE / Debranching / metal ions / RNA
Function / homology
Function and homology information
RNA lariat debranching enzyme activity / Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases / RNA splicing, via transesterification reactions / mRNA splicing, via spliceosome / manganese ion binding / iron ion binding / perinuclear region of cytoplasm / RNA binding / zinc ion binding / nucleus Similarity search - Function
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
ID
Wavelength (Å)
Relative weight
1
1.1
1
2
1.28
1
3
1.3
1
Reflection
Resolution: 1.8→50 Å / Num. obs: 35775 / % possible obs: 100 % / Redundancy: 12.1 % / Rmerge(I) obs: 0.074 / Χ2: 0.74 / Net I/σ(I): 34.1
Reflection shell
Resolution: 1.8→1.85 Å / Redundancy: 12.2 % / Rmerge(I) obs: 0.529 / Mean I/σ(I) obs: 3.81 / Num. unique obs: 413 / Χ2: 0.474 / % possible all: 100
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Processing
Software
Name
Version
Classification
REFMAC
5.7.0029
refinement
HKL-2000
datareduction
SCALEPACK
datascaling
SHELXCD
phasing
Refinement
Method to determine structure: SAD / Resolution: 1.8→41.88 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.959 / SU B: 2.842 / SU ML: 0.087 / Cross valid method: THROUGHOUT / ESU R: 0.131 / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.21027
1616
5.1 %
RANDOM
Rwork
0.17197
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obs
0.17393
30215
95.29 %
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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