Salmonella outer protein D / Salmonella outer protein D / protein secretion by the type III secretion system / host cell cytosol / host cell membrane / host cell plasma membrane / extracellular region / membrane / Secreted effector protein SopD
Function and homology information
Biological species
Salmonella typhimurium (bacteria)
Method
X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.15 Å
Type: MAR CCD 165 mm / Detector: CCD / Date: Jul 10, 2011
Radiation
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.9793 Å / Relative weight: 1
Reflection
Resolution: 2.15→50 Å / Num. obs: 37360 / % possible obs: 99 % / Redundancy: 7.5 % / Rmerge(I) obs: 0.064 / Χ2: 2.245 / Net I/av σ(I): 54.3 / Net I/σ(I): 17.4 / Num. measured all: 280209
Reflection shell
Diffraction-ID: 1 / Rejects: _
Resolution (Å)
Redundancy (%)
Rmerge(I) obs
Num. unique all
Χ2
% possible all
2.15-2.23
7.6
0.521
3761
1.218
100
2.23-2.32
7.6
0.39
3745
1.245
100
2.32-2.42
7.7
0.257
3758
1.249
100
2.42-2.55
7.7
0.183
3746
1.352
100
2.55-2.71
7.7
0.126
3778
1.475
100
2.71-2.92
7.7
0.086
3771
1.663
100
2.92-3.21
7.7
0.071
3756
2.358
100
3.21-3.68
7.2
0.065
3785
4.091
100
3.68-4.63
6.9
0.057
3766
4.81
99.8
4.63-50
7.2
0.045
3494
3.572
90.7
-
Processing
Software
Name
Version
Classification
HKL-2000
datascaling
REFMAC
5.5.0109
refinement
PDB_EXTRACT
3.15
dataextraction
HKL-2000
datareduction
SHARP
phasing
Refinement
Method to determine structure: SAD / Resolution: 2.15→50 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.941 / WRfactor Rfree: 0.2555 / WRfactor Rwork: 0.2225 / FOM work R set: 0.8022 / SU B: 14.162 / SU ML: 0.162 / SU R Cruickshank DPI: 0.2405 / SU Rfree: 0.1916 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.24 / ESU R Free: 0.192 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.2434
1867
5 %
RANDOM
Rwork
0.2122
-
-
-
obs
0.2138
35455
98.76 %
-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
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