- PDB-4ezb: CRYSTAL STRUCTURE OF the Conserved hypothetical protein from Sino... -
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Basic information
Entry
Database: PDB / ID: 4ezb
Title
CRYSTAL STRUCTURE OF the Conserved hypothetical protein from Sinorhizobium meliloti 1021
Components
uncharacterized conserved protein
Keywords
Structural Genomics / Unknown Function / PROTEIN STRUCTURE INITIATIVE / NEW YORK STRUCTURAL GENOMIX RESEARCH CONSORTIUM / NYSGRC / conserved protein / PSI-Biology / New York Structural Genomics Research Consortium
Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.9791 Å / Relative weight: 1
Reflection
Redundancy: 3.2 % / Av σ(I) over netI: 17.02 / Number: 99839 / Rmerge(I) obs: 0.086 / Χ2: 1.48 / D res high: 2.1 Å / D res low: 50 Å / Num. obs: 30844 / % possible obs: 94.1
Diffraction reflection shell
Highest resolution (Å)
Lowest resolution (Å)
% possible obs (%)
ID
Rmerge(I) obs
Chi squared
Redundancy
5.7
50
99.3
1
0.04
2.981
3.5
4.52
5.7
99.7
1
0.05
2.946
3.4
3.95
4.52
99.9
1
0.059
3.171
3.4
3.59
3.95
99.9
1
0.069
2.538
3.5
3.33
3.59
100
1
0.077
1.8
3.5
3.14
3.33
99.9
1
0.097
1.459
3.5
2.98
3.14
99.9
1
0.116
1.194
3.5
2.85
2.98
100
1
0.159
1.15
3.5
2.74
2.85
100
1
0.209
1.066
3.6
2.65
2.74
100
1
0.298
0.947
3.5
2.56
2.65
100
1
0.337
0.888
3.5
2.49
2.56
99.9
1
0.416
0.9
3.5
2.42
2.49
100
1
0.449
0.814
3.4
2.37
2.42
99.8
1
0.507
0.844
3.3
2.31
2.37
97.8
1
0.519
0.854
3
2.26
2.31
93.6
1
0.643
0.836
2.8
2.22
2.26
90.3
1
0.565
0.789
2.5
2.18
2.22
77
1
0.593
0.763
2.2
2.14
2.18
68.8
1
0.652
0.813
2.2
2.1
2.14
56.5
1
0.675
0.714
2.1
Reflection
Resolution: 2.1→50 Å / Num. obs: 30844 / % possible obs: 94.1 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.086 / Χ2: 1.477 / Net I/σ(I): 8.4
Reflection shell
Resolution (Å)
Redundancy (%)
Rmerge(I) obs
Num. unique all
Χ2
Diffraction-ID
% possible all
2.1-2.14
2.1
0.675
943
0.714
1
56.5
2.14-2.18
2.2
0.652
1105
0.813
1
68.8
2.18-2.22
2.2
0.593
1291
0.763
1
77
2.22-2.26
2.5
0.565
1459
0.789
1
90.3
2.26-2.31
2.8
0.643
1546
0.836
1
93.6
2.31-2.37
3
0.519
1565
0.854
1
97.8
2.37-2.42
3.3
0.507
1693
0.844
1
99.8
2.42-2.49
3.4
0.449
1580
0.814
1
100
2.49-2.56
3.5
0.416
1655
0.9
1
99.9
2.56-2.65
3.5
0.337
1643
0.888
1
100
2.65-2.74
3.5
0.298
1661
0.947
1
100
2.74-2.85
3.6
0.209
1613
1.066
1
100
2.85-2.98
3.5
0.159
1650
1.15
1
100
2.98-3.14
3.5
0.116
1623
1.194
1
99.9
3.14-3.33
3.5
0.097
1629
1.459
1
99.9
3.33-3.59
3.5
0.077
1645
1.8
1
100
3.59-3.95
3.5
0.069
1650
2.538
1
99.9
3.95-4.52
3.4
0.059
1633
3.171
1
99.9
4.52-5.7
3.4
0.05
1642
2.946
1
99.7
5.7-50
3.5
0.04
1618
2.981
1
99.3
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Phasing
Phasing
Method: SAD
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Processing
Software
Name
Version
Classification
NB
SCALEPACK
datascaling
REFMAC
refinement
PDB_EXTRACT
3.11
dataextraction
CBASS
datacollection
HKL-3000
datareduction
PHENIX
phasing
Refinement
Method to determine structure: SAD / Resolution: 2.1→19.09 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.95 / WRfactor Rfree: 0.2327 / WRfactor Rwork: 0.1801 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8059 / SU B: 14.366 / SU ML: 0.176 / SU R Cruickshank DPI: 0.247 / SU Rfree: 0.2018 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.247 / ESU R Free: 0.202 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.2442
808
5 %
RANDOM
Rwork
0.1931
-
-
-
obs
0.1957
16270
96.19 %
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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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