- PDB-3nbm: The lactose-specific IIB component domain structure of the phosph... -
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Basic information
Entry
Database: PDB / ID: 3nbm
Title
The lactose-specific IIB component domain structure of the phosphoenolpyruvate:carbohydrate phosphotransferase system (PTS) from Streptococcus pneumoniae.
Components
PTS system, lactose-specific IIBC components
Keywords
TRANSFERASE / PTS_IIB_lactose / phosphoenolpyruvate:carbohydrate system / P-loop / phosphorylation / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.97934 Å / Relative weight: 1
Reflection
Redundancy: 13.3 % / Av σ(I) over netI: 55.24 / Number: 284542 / Rmerge(I) obs: 0.072 / Χ2: 2.15 / D res high: 1.3 Å / D res low: 50 Å / Num. obs: 21377 / % possible obs: 97.3
D res high: 1.3 Å / D res low: 38.15 Å / FOM : 0.236 / FOM acentric: 0.28 / FOM centric: 0 / Reflection: 21276 / Reflection acentric: 17906 / Reflection centric: 3370
Phasing MAD set
R cullis acentric: 1.68 / R cullis centric: 1 / Highest resolution: 1.3 Å / Lowest resolution: 38.15 Å / Loc acentric: 0.1 / Loc centric: 0.1 / Power acentric: 0 / Power centric: 0 / Reflection acentric: 17906 / Reflection centric: 3370
Phasing MAD set shell
ID: 1 / R cullis centric: 1 / Power acentric: 0 / Power centric: 0
Resolution (Å)
R cullis acentric
Loc acentric
Loc centric
Reflection acentric
Reflection centric
8.4-38.15
1.31
0.3
0.2
35
61
4.72-8.4
1.75
0.3
0.2
262
182
3.28-4.72
1.14
0.2
0.2
683
283
2.51-3.28
1.44
0.2
0.1
1335
397
2.04-2.51
1.47
0.1
0.1
2188
501
1.71-2.04
1.87
0.1
0
3239
598
1.48-1.71
2.4
0
0
4539
702
1.3-1.48
4.08
0
0
5625
646
Phasing MAD set site
Atom type symbol: Se / Occupancy iso: 0
ID
B iso
Fract x
Fract y
Fract z
Occupancy
1
19.4581
-0.681
-0.913
-0.045
3.97
2
20.3965
-0.937
-1.043
-0.096
3.929
3
20.2329
-0.917
-0.921
-0.13
3.204
4
12.481
-1.153
-0.904
-0.047
0.143
Phasing MAD shell
Resolution (Å)
FOM
FOM acentric
FOM centric
Reflection
Reflection acentric
Reflection centric
8.4-38.15
0.191
0.525
0
96
35
61
4.72-8.4
0.346
0.586
0
444
262
182
3.28-4.72
0.338
0.478
0
966
683
283
2.51-3.28
0.393
0.51
0
1732
1335
397
2.04-2.51
0.313
0.384
0
2689
2188
501
1.71-2.04
0.285
0.338
0
3837
3239
598
1.48-1.71
0.22
0.254
0
5241
4539
702
1.3-1.48
0.12
0.134
0
6271
5625
646
Phasing dm
Method: Solvent flattening and Histogram matching / Reflection: 21276
Phasing dm shell
Resolution (Å)
Delta phi final
FOM
Reflection
4.81-100
69.6
0.769
508
3.77-4.81
65.7
0.874
509
3.27-3.77
67.2
0.86
508
2.96-3.27
62.9
0.866
503
2.73-2.96
69.4
0.843
530
2.54-2.73
64.1
0.828
570
2.39-2.54
66.4
0.83
608
2.27-2.39
63.8
0.804
625
2.16-2.27
68.1
0.815
668
2.06-2.16
66.9
0.788
690
1.98-2.06
62
0.819
714
1.91-1.98
69.5
0.799
761
1.84-1.91
67.3
0.789
771
1.78-1.84
67.2
0.779
788
1.73-1.78
69.4
0.754
818
1.68-1.73
73.1
0.754
852
1.63-1.68
71.8
0.746
881
1.59-1.63
72.8
0.715
860
1.55-1.59
71.9
0.7
927
1.51-1.55
75.4
0.704
941
1.48-1.51
77.1
0.689
934
1.45-1.48
73.9
0.68
981
1.42-1.45
80.1
0.685
987
1.39-1.42
77.2
0.657
979
1.36-1.39
84.6
0.657
948
1.34-1.36
81.8
0.65
930
1.3-1.34
84.9
0.621
1485
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Processing
Software
Name
Version
Classification
NB
DENZO
datareduction
SCALEPACK
datascaling
MLPHARE
phasing
DM
6
phasing
REFMAC
refinement
PDB_EXTRACT
3.1
dataextraction
SBC-Collect
datacollection
HKL-3000
datareduction
HKL-3000
datascaling
HKL-3000
phasing
SHELXD
phasing
SHELXE
modelbuilding
SOLVE
phasing
RESOLVE
phasing
ARP/wARP
modelbuilding
CCP4
phasing
O
modelbuilding
Coot
modelbuilding
Refinement
Method to determine structure: SAD / Resolution: 1.3→25.15 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.969 / WRfactor Rfree: 0.167 / WRfactor Rwork: 0.131 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.933 / SU B: 1.321 / SU ML: 0.026 / SU R Cruickshank DPI: 0.054 / SU Rfree: 0.05 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.05 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.167
1096
5.2 %
RANDOM
Rwork
0.132
-
-
-
all
0.134
21193
-
-
obs
0.134
21193
96.95 %
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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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