- PDB-3ooa: Crystal structures and biochemical characterization of the bacter... -
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Basic information
Entry
Database: PDB / ID: 3ooa
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: 2.04→33.75 Å / Num. obs: 57305 / % possible obs: 98.4 % / Observed criterion σ(I): -3 / Redundancy: 3.3 % / Biso Wilson estimate: 23.568 Å2 / Rmerge(I) obs: 0.104 / Net I/σ(I): 9.48
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
2.04-2.09
0.747
0.538
2.2
11621
4277
4119
0.655
96.3
2.09-2.15
0.623
0.449
2.6
11726
4190
4064
0.547
97
2.15-2.21
0.501
0.371
3.2
11520
4047
3942
0.451
97.4
2.21-2.28
0.437
0.33
3.6
11716
3982
3890
0.399
97.7
2.28-2.36
0.377
0.293
4.1
11229
3754
3664
0.354
97.6
2.36-2.44
0.308
0.243
4.9
11488
3745
3672
0.293
98.1
2.44-2.53
0.28
0.221
5.4
11225
3531
3485
0.265
98.7
2.53-2.63
0.225
0.184
6.6
11298
3503
3450
0.22
98.5
2.63-2.75
0.183
0.156
7.8
10910
3273
3226
0.185
98.6
2.75-2.89
0.162
0.132
9.1
10799
3150
3120
0.157
99
2.89-3.04
0.122
0.106
11.2
10437
3009
2981
0.126
99.1
3.04-3.23
0.093
0.085
13.8
10193
2846
2821
0.1
99.1
3.23-3.45
0.07
0.07
16.6
9658
2656
2648
0.082
99.7
3.45-3.72
0.058
0.061
18.7
9209
2505
2500
0.072
99.8
3.72-4.08
0.049
0.054
20.7
8499
2305
2300
0.063
99.8
4.08-4.56
0.048
0.053
21.5
7716
2090
2086
0.062
99.8
4.56-5.27
0.047
0.05
20.8
6888
1837
1835
0.058
99.9
5.27-6.45
0.052
0.051
18.9
6024
1605
1605
0.06
100
6.45-9.12
0.036
0.036
22.5
4456
1208
1208
0.043
100
9.12
0.027
0.026
25.3
2402
707
689
0.031
97.5
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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: 2.04→33.75 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.912 / WRfactor Rfree: 0.2088 / WRfactor Rwork: 0.1544 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8685 / SU B: 4.044 / SU ML: 0.11 / SU R Cruickshank DPI: 0.1844 / SU Rfree: 0.1703 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.17 / 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
0.2255
2866
5 %
RANDOM
Rwork
0.1675
-
-
-
obs
0.1704
54440
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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