- PDB-3lyk: Structure of stringent starvation protein A homolog from Haemophi... -
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Open data
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Basic information
Entry
Database: PDB / ID: 3lyk
Title
Structure of stringent starvation protein A homolog from Haemophilus influenzae
Components
Stringent starvation protein A homolog
Keywords
TRANSPORT PROTEIN / structural genomics / GST-superfamily / sspA / Stringent starvation protein A homolog / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.9793 Å / Relative weight: 1
Reflection
Resolution: 2.1→30 Å / Num. obs: 41914 / % possible obs: 100 % / Redundancy: 9.8 % / Rmerge(I) obs: 0.141 / Χ2: 1.233 / Net I/σ(I): 7.2
Reflection shell
Resolution (Å)
Redundancy (%)
Rmerge(I) obs
Num. unique all
Χ2
% possible all
2.1-2.14
9.8
0.801
2079
0.843
100
2.14-2.18
9.9
0.747
2071
0.862
100
2.18-2.22
9.9
0.639
2045
0.862
100
2.22-2.26
9.9
0.566
2095
0.898
100
2.26-2.31
9.9
0.493
2078
0.863
100
2.31-2.37
9.9
0.441
2054
0.904
100
2.37-2.42
9.9
0.39
2117
0.902
100
2.42-2.49
9.9
0.334
2040
0.939
100
2.49-2.56
9.9
0.272
2078
1.011
100
2.56-2.65
9.9
0.262
2090
1.012
100
2.65-2.74
9.9
0.221
2094
1.056
100
2.74-2.85
9.9
0.188
2072
1.116
100
2.85-2.98
9.9
0.159
2103
1.217
100
2.98-3.14
9.9
0.143
2092
1.333
100
3.14-3.33
9.8
0.115
2083
1.432
100
3.33-3.59
9.8
0.099
2106
1.566
100
3.59-3.95
9.7
0.094
2111
1.668
100
3.95-4.52
9.6
0.09
2129
1.801
100
4.52-5.69
9.2
0.082
2148
2.043
100
5.69-30
9.1
0.081
2229
2.396
100
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Processing
Software
Name
Version
Classification
NB
DENZO
datareduction
SCALEPACK
datascaling
REFMAC
refinement
PDB_EXTRACT
3.005
dataextraction
CBASS
datacollection
HKL-2000
datareduction
PHENIX
phasing
CCP4
phasing
Refinement
Method to determine structure: SAD / Resolution: 2.1→30 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.931 / WRfactor Rfree: 0.228 / WRfactor Rwork: 0.198 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.846 / SU B: 3.789 / SU ML: 0.101 / SU R Cruickshank DPI: 0.153 / SU Rfree: 0.146 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.153 / ESU R Free: 0.146 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS, U VALUES REFINED INDIVIDUALLY, UNKNOWN DENSITY OBSERVED BETWEEN RESIDUES ARG-105 and TRP-110 SIDECHAINS OF BOTH THE MOLECULES A ANF B.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.237
2109
5 %
RANDOM
Rwork
0.202
-
-
-
obs
0.204
41786
99.66 %
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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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