- PDB-6gz8: First GerMN domain of the sporulation protein GerM from Bacillus ... -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 6gz8
Title
First GerMN domain of the sporulation protein GerM from Bacillus subtilis
Components
Spore germination protein GerM
Keywords
STRUCTURAL PROTEIN / GerM / GerMN domain / lipoprotein / sporulation / endospores / secretion systems
Function / homology
GerMN domain / Sporulation and spore germination / Sporulation and spore germination / sporulation resulting in formation of a cellular spore / Prokaryotic membrane lipoprotein lipid attachment site profile. / Spore germination protein GerM
Function and homology information
Biological species
Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Method
X-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1 Å
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.97242 Å / Relative weight: 1
Reflection
Resolution: 1→50 Å / Num. obs: 68958 / % possible obs: 94.5 % / Redundancy: 3.6 % / Biso Wilson estimate: 10.46 Å2 / Rrim(I) all: 0.07 / Rsym value: 0.061 / Net I/σ(I): 11.22
Reflection shell
Resolution: 1→1.06 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 2.95 / Num. unique obs: 10428 / Rrim(I) all: 0.42 / Rsym value: 0.356 / % possible all: 90.4
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Processing
Software
Name
Version
Classification
REFMAC
5.8.0189
refinement
XDS
datareduction
XSCALE
datascaling
Arcimboldo
phasing
Refinement
Method to determine structure: AB INITIO PHASING / Resolution: 1→41.32 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.978 / SU B: 0.806 / SU ML: 0.018 / Cross valid method: FREE R-VALUE / ESU R: 0.021 / ESU R Free: 0.022 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.15364
1738
2.5 %
RANDOM
Rwork
0.13453
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obs
0.13499
67101
94.48 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å