IMMUNE SYSTEM / IMMUNOGLOBULIN DOMAIN / GLYCOPROTEIN / DISULFIDE BOND / IMMUNITY / ADAPTIVE IMMUNITY / Structural Genomics / PSI-Biology / Protein Structure Initiative / New York Structural Genomics Research Consortium / NYSGRC / IMMUNOGLOBULIN VARIABLE-LIKE DOMAIN / CELL SURFACE / Atoms-to-Animals: The Immune Function Network / IFN
Function / homology
Function and homology information
interleukin-4 production / response to protozoan / type II interferon production / negative regulation of T cell activation / regulation of immune response / negative regulation of T cell proliferation / positive regulation of T cell proliferation / regulation of cytokine production / positive regulation of interleukin-2 production / T cell receptor signaling pathway ...interleukin-4 production / response to protozoan / type II interferon production / negative regulation of T cell activation / regulation of immune response / negative regulation of T cell proliferation / positive regulation of T cell proliferation / regulation of cytokine production / positive regulation of interleukin-2 production / T cell receptor signaling pathway / adaptive immune response / membrane => GO:0016020 / external side of plasma membrane / signaling receptor binding / negative regulation of apoptotic process Similarity search - Function
Monochromator: Si crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
ID
Wavelength (Å)
Relative weight
1
1.075
1
2
1.5402
1
Reflection
Redundancy: 18.4 % / Av σ(I) over netI: 4.3 / Number: 201521 / Rsym value: 0.161 / D res high: 1.793 Å / D res low: 43.145 Å / Num. obs: 10948 / % possible obs: 86.4
Diffraction reflection shell
Highest resolution (Å)
Lowest resolution (Å)
% possible obs (%)
ID
Rmerge(I) obs
Rsym value
Redundancy
5.67
38.72
99.6
1
0.069
0.069
18.8
4.01
5.67
100
1
0.062
0.062
20.5
3.27
4.01
75.3
1
0.084
0.084
17.4
2.84
3.27
100
1
0.099
0.099
17.1
2.54
2.84
86.8
1
0.152
0.152
17.1
2.31
2.54
99.6
1
0.208
0.208
17.3
2.14
2.31
83
1
0.408
0.408
17.8
2
2.14
83.1
1
0.472
0.472
18.9
1.89
2
66.7
1
1.016
1.016
19.6
1.79
1.89
89.4
1
1.792
1.792
19.7
Reflection
Resolution: 1.59→43.149 Å / Num. all: 17917 / Num. obs: 16143 / % possible obs: 90.1 % / Redundancy: 13.3 % / Biso Wilson estimate: 13.046 Å2 / Rsym value: 0.088 / Net I/σ(I): 17.7
Reflection shell
Diffraction-ID: 1,2
Resolution (Å)
Redundancy (%)
Mean I/σ(I) obs
Num. measured all
Num. unique all
Rsym value
% possible all
1.59-1.68
13.5
1.6
34525
2548
0.489
100
1.68-1.78
14.1
2.4
30517
2159
0.315
89.6
1.78-1.9
13.9
3.8
29235
2109
0.198
93
1.9-2.05
13.4
5.3
22648
1687
0.128
78.8
2.05-2.25
13.1
6.1
21182
1616
0.113
81.9
2.25-2.52
12.8
7.6
21479
1674
0.088
92.9
2.52-2.9
12.5
8.5
18089
1449
0.073
89.9
2.9-3.56
12.2
8.7
15743
1286
0.07
93.5
3.56-5.03
12.7
11.3
11980
942
0.053
85.5
5.03-38.59
12.7
13.9
8555
673
0.042
98.9
-
Phasing
Phasing
Method: SIRAS
Phasing MAD set site
ID
Cartn x (Å)
Cartn y (Å)
Cartn z (Å)
Atom type symbol
B iso
Occupancy
1
30.992
23.737
10.724
S
20
1
2
33.251
24.087
16.194
S
20
0.58
3
28.327
27.525
14.529
S
20
0.34
4
30.695
43.659
17.143
S
20
0.16
5
28.033
21.911
1.079
S
20
0.15
6
30.508
18.504
2.543
S
20
0.14
7
33.445
45.949
15.446
S
20
0.1
8
32.369
22.256
5.436
S
20
0.08
9
32.418
23.803
23.98
S
20
0.08
10
28.911
45.261
11.786
S
20
0.06
11
37.866
54.336
8.5
S
20
0.02
-
Processing
Software
Name
Version
Classification
NB
SCALA
3.3.20
datascaling
SHELX
phasing
REFMAC
refinement
PDB_EXTRACT
3.11
dataextraction
CBASS
datacollection
MOSFLM
datareduction
SHELXD
phasing
Refinement
Method to determine structure: SIRAS / Resolution: 1.59→19.91 Å / WRfactor Rfree: 0.1935 / WRfactor Rwork: 0.177 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.9077 / SU B: 1.216 / SU ML: 0.044 / SU R Cruickshank DPI: 0.0905 / SU Rfree: 0.0847 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.09 / ESU R Free: 0.085 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; U VALUES HAVE BEEN REFINED INDIVIDUALLY
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.1916
837
5.2 %
RANDOM
Rwork
0.1741
-
-
-
obs
0.175
15194
89.82 %
-
all
-
16916
-
-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
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