- PDB-2wcq: Crystal Structure of Tip-Alpha N34 (HP0596) from Helicobacter pyl... -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 2wcq
Title
Crystal Structure of Tip-Alpha N34 (HP0596) from Helicobacter pylori at pH4
Components
TNF-ALPHA INDUCER PROTEIN
Keywords
IMMUNE SYSTEM / HP0596 / TIP-ALPHA / HELICOBACTER PYLORI
Function / homology
Helicobacter TNF-alpha-Inducing protein / Helicobacter TNF-alpha-inducing protein / TNF-alpha-Inducing protein of Helicobacter / Thiol Ester Dehydrase; Chain A / Prokaryotic membrane lipoprotein lipid attachment site profile. / Roll / Alpha Beta / CITRIC ACID / Tumor necrosis factor alpha-inducing protein
Function and homology information
Biological species
HELICOBACTER PYLORI (bacteria)
Method
X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
Monochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.9395 Å / Relative weight: 1
Reflection
Resolution: 1.8→50.96 Å / Num. obs: 22965 / % possible obs: 98.4 % / Observed criterion σ(I): 2 / Redundancy: 4.08 % / Biso Wilson estimate: 25.2 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 7.62
Reflection shell
Resolution: 1.9→2 Å / Redundancy: 3.56 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 2.23 / % possible all: 90.4
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Processing
Software
Name
Version
Classification
REFMAC
5.5.0070
refinement
MOSFLM
datareduction
SCALA
datascaling
SHARP
phasing
Refinement
Method to determine structure: SAD Starting model: NONE Resolution: 1.9→47.14 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.933 / SU B: 3.51 / SU ML: 0.103 / Cross valid method: THROUGHOUT / ESU R: 0.171 / ESU R Free: 0.151 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.231
1180
5.1 %
RANDOM
Rwork
0.195
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obs
0.197
21752
98.3 %
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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