Type II/IV secretion system protein / Type II/IV secretion system protein / Large family of predicted nucleotide-binding domains / PIN domain / P-loop containing nucleoside triphosphate hydrolase / Nucleotide binding protein PINc
Function and homology information
Biological species
Sulfolobus islandicus (acidophilic)
Method
X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.699 Å
Mass: 18.015 Da / Num. of mol.: 230 / Source method: isolated from a natural source / Formula: H2O
-
Experimental details
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Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
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Sample preparation
Crystal
Density Matthews: 2.61 Å3/Da / Density % sol: 52.94 %
Crystal grow
Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5 Details: 3:2 ratio of protein to mother liquor (0.1 M sodium malonate pH 5.0, 12% PEG 3350, 3% glycerol)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.97 Å / Relative weight: 1
Reflection
Resolution: 2.699→39.19 Å / Num. all: 96879 / Num. obs: 89886 / % possible obs: 97.63 % / Redundancy: 7 % / Rmerge(I) obs: 0.145 / Net I/σ(I): 16.1
Reflection shell
Resolution: 2.699→2.769 Å / Redundancy: 6.6 % / Rmerge(I) obs: 2.453 / Mean I/σ(I) obs: 4.3 / % possible all: 92.67
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Phasing
Phasing dm
Method: Solvent flattening and Histogram matching / Reflection: 94618
Phasing dm shell
Resolution (Å)
Delta phi final
FOM
Reflection
14.63-100
33.5
0.823
612
10.35-14.63
33.4
0.892
1108
8.45-10.35
31.1
0.924
1414
7.32-8.45
36.6
0.88
1698
6.54-7.32
35.6
0.864
1948
5.97-6.54
34.4
0.868
2143
5.53-5.97
29.2
0.894
2345
5.17-5.53
25.8
0.902
2358
4.88-5.17
22.1
0.916
2597
4.63-4.88
19.7
0.934
2772
4.41-4.63
17.9
0.941
2938
4.22-4.41
19
0.931
3058
4.06-4.22
21.2
0.919
3223
3.91-4.06
21.6
0.895
3295
3.78-3.91
21.6
0.891
3428
3.66-3.78
21.9
0.896
3454
3.55-3.66
23.5
0.881
3511
3.45-3.55
25.2
0.874
3704
3.36-3.45
25.2
0.842
3827
3.27-3.36
25.6
0.886
3945
3.19-3.27
26.5
0.892
4117
3.12-3.19
27.8
0.875
4165
3.05-3.12
27.9
0.87
4268
2.99-3.05
30.2
0.865
4376
2.93-2.99
31.2
0.858
4467
2.87-2.93
33.7
0.833
4548
2.82-2.87
35.7
0.808
4547
2.77-2.82
39.5
0.763
4509
2.7-2.77
42.4
0.737
6243
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Processing
Software
Name
Version
Classification
REFMAC
refinement
PDB_EXTRACT
3.15
dataextraction
XDS
datareduction
XDS
datascaling
PHASER
phasing
Coot
0.8.2
modelbuilding
Blu-Ice
datacollection
Refinement
Method to determine structure: MAD / Resolution: 2.699→39.19 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.922 / WRfactor Rfree: 0.2169 / WRfactor Rwork: 0.182 / FOM work R set: 0.6575 / SU B: 48.41 / SU ML: 0.405 / SU R Cruickshank DPI: 0.9767 / SU Rfree: 0.3491 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.977 / ESU R Free: 0.349 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.265
4732
5 %
RANDOM
Rwork
0.2274
-
-
-
obs
0.2293
89886
97.63 %
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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
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