- PDB-3oo9: Crystal structures and biochemical characterization of the bacter... -
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Open data
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Basic information
Entry
Database: PDB / ID: 3oo9
Title
Crystal structures and biochemical characterization of the bacterial solute receptor AcbH reveal an unprecedented exclusive substrate preference for b-D-galactopyranose
Components
ABC transporter binding protein AcbH
Keywords
SUGAR BINDING PROTEIN / class 2 SBP fold / ABC transporter extracellular solute binding protein / D-galactose Binding
Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.91841 Å / Relative weight: 1
Reflection
Resolution: 1.76→33.71 Å / Num. obs: 84900 / % possible obs: 94.4 % / Observed criterion σ(I): -3 / Redundancy: 2.8 % / Biso Wilson estimate: 20.134 Å2 / Rmerge(I) obs: 0.092 / Net I/σ(I): 8.78
Reflection shell
Diffraction-ID: 1
Resolution (Å)
Highest resolution (Å)
Rmerge F obs
Rmerge(I) obs
Mean I/σ(I) obs
Num. measured obs
Num. possible
Num. unique obs
Rrim(I) all
% possible all
1.76-1.81
0.82
0.553
1.8
13578
6633
5881
0.69
88.7
1.81-1.86
0.651
0.445
2.2
13634
6481
5806
0.554
89.6
1.86-1.91
0.586
0.406
2.5
13589
6245
5703
0.505
91.3
1.91-1.97
0.439
0.311
3.2
13673
6128
5651
0.387
92.2
1.97-2.03
0.366
0.253
3.9
13605
5846
5440
0.313
93.1
2.03-2.1
0.279
0.203
4.9
13710
5731
5381
0.25
93.9
2.1-2.18
0.244
0.173
5.8
13759
5593
5292
0.214
94.6
2.18-2.27
0.204
0.152
6.7
13571
5255
5023
0.187
95.6
2.27-2.37
0.18
0.136
7.5
13579
5073
4899
0.167
96.6
2.37-2.49
0.157
0.12
8.4
13425
4892
4729
0.147
96.7
2.49-2.62
0.139
0.11
9.4
13313
4690
4530
0.135
96.6
2.62-2.78
0.111
0.092
11
12819
4354
4246
0.112
97.5
2.78-2.97
0.096
0.083
12.4
12549
4134
4050
0.1
98
2.97-3.21
0.075
0.07
15.3
12062
3864
3786
0.083
98
3.21-3.52
0.059
0.06
18.2
11266
3556
3460
0.072
97.3
3.52-3.94
0.047
0.051
20.6
10320
3231
3145
0.06
97.3
3.94-4.54
0.04
0.045
22.4
9053
2826
2752
0.053
97.4
4.54-5.57
0.039
0.044
22.1
7963
2436
2353
0.052
96.6
5.57-7.87
0.04
0.042
21
6107
1888
1799
0.05
95.3
7.87
0.024
0.026
25
3221
1061
974
0.031
91.8
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Processing
Software
Name
Version
Classification
NB
XSCALE
datascaling
REFMAC
refinement
PDB_EXTRACT
3.1
dataextraction
ADSC
Quantum
datacollection
PHASER
phasing
Refinement
Method to determine structure: MOLECULAR REPLACEMENT Starting model: model from SeMet SAD phasing Resolution: 1.76→33.71 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.938 / WRfactor Rfree: 0.1808 / WRfactor Rwork: 0.1426 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8906 / SU B: 2.217 / SU ML: 0.069 / SU R Cruickshank DPI: 0.1047 / SU Rfree: 0.1051 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.105 / 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
0.1948
4245
5 %
RANDOM
Rwork
0.155
-
-
-
obs
0.157
84899
100 %
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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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