indoleamine 2,3-dioxygenase / smooth muscle contractile fiber / indoleamine 2,3-dioxygenase activity / positive regulation of chronic inflammatory response / kynurenic acid biosynthetic process / tryptophan 2,3-dioxygenase activity / positive regulation of T cell tolerance induction / tryptophan catabolic process to kynurenine / stereocilium bundle / positive regulation of type 2 immune response ... indoleamine 2,3-dioxygenase / smooth muscle contractile fiber / indoleamine 2,3-dioxygenase activity / positive regulation of chronic inflammatory response / kynurenic acid biosynthetic process / tryptophan 2,3-dioxygenase activity / positive regulation of T cell tolerance induction / tryptophan catabolic process to kynurenine / stereocilium bundle / positive regulation of type 2 immune response / 'de novo' NAD biosynthetic process from tryptophan / tryptophan catabolic process / Tryptophan catabolism / negative regulation of T cell apoptotic process / positive regulation of T cell apoptotic process / swimming behavior / negative regulation of interleukin-10 production / multicellular organismal response to stress / negative regulation of T cell proliferation / T cell proliferation / positive regulation of interleukin-12 production / female pregnancy / response to lipopolysaccharide / electron transfer activity / inflammatory response / heme binding / metal ion binding / cytosol / cytoplasm Similarity search - Function
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 1.5418 Å / Relative weight: 1
Reflection
Resolution: 2.285→19.76 Å / Num. obs: 54213 / % possible obs: 88.6 % / Redundancy: 3.7 % / CC1/2: 0.998 / Net I/σ(I): 11.8
Reflection shell
Resolution: 2.285→2.62 Å / Redundancy: 3.03 % / Mean I/σ(I) obs: 1.8 / Num. unique obs: 2708 / CC1/2: 0.537 / % possible all: 45.3
-
Processing
Software
Name
Classification
BUSTER
refinement
autoPROC
datareduction
autoPROC
datascaling
PHASER
phasing
Refinement
Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.285→19.76 Å / Cor.coef. Fo:Fc: 0.881 / Cor.coef. Fo:Fc free: 0.857 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.844 / SU Rfree Blow DPI: 0.37 Details: HYDROGENS WERE FULLY REFINED WITH ZERO OCCUPANCY AT NUCLEAR POSITION.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.2999
2839
5.24 %
RANDOM
Rwork
0.279
-
-
-
obs
0.28
54213
56.6 %
-
Displacement parameters
Biso mean: 61.37 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-3.4174 Å2
0 Å2
-0.2975 Å2
2-
-
6.4833 Å2
0 Å2
3-
-
-
-3.0658 Å2
Refine analyze
Luzzati coordinate error obs: 0.49 Å
Refinement step
Cycle: LAST / Resolution: 2.285→19.76 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
11124
0
140
317
11581
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
Restraint function
Weight
X-RAY DIFFRACTION
t_bond_d
0.007
22454
HARMONIC
2
X-RAY DIFFRACTION
t_angle_deg
0.84
40545
HARMONIC
2
X-RAY DIFFRACTION
t_dihedral_angle_d
6510
SINUSOIDAL
2
X-RAY DIFFRACTION
t_incorr_chiral_ct
X-RAY DIFFRACTION
t_pseud_angle
X-RAY DIFFRACTION
t_trig_c_planes
X-RAY DIFFRACTION
t_gen_planes
3576
HARMONIC
5
X-RAY DIFFRACTION
t_it
11540
HARMONIC
10
X-RAY DIFFRACTION
t_nbd
X-RAY DIFFRACTION
t_omega_torsion
2.41
X-RAY DIFFRACTION
t_other_torsion
17.15
X-RAY DIFFRACTION
t_improper_torsion
X-RAY DIFFRACTION
t_chiral_improper_torsion
1465
SEMIHARMONIC
5
X-RAY DIFFRACTION
t_sum_occupancies
X-RAY DIFFRACTION
t_utility_distance
X-RAY DIFFRACTION
t_utility_angle
X-RAY DIFFRACTION
t_utility_torsion
X-RAY DIFFRACTION
t_ideal_dist_contact
16521
SEMIHARMONIC
4
LS refinement shell
Resolution: 2.29→2.48 Å / Total num. of bins used: 51
Rfactor
Num. reflection
% reflection
Rfree
0.4236
-
5.62 %
Rwork
0.3954
1024
-
all
0.397
1085
-
obs
-
-
5.31 %
Refinement TLS params.
Method: refined / Refine-ID: X-RAY DIFFRACTION
ID
L11 (°2)
L12 (°2)
L13 (°2)
L22 (°2)
L23 (°2)
L33 (°2)
S11 (Å °)
S12 (Å °)
S13 (Å °)
S21 (Å °)
S22 (Å °)
S23 (Å °)
S31 (Å °)
S32 (Å °)
S33 (Å °)
T11 (Å2)
T12 (Å2)
T13 (Å2)
T22 (Å2)
T23 (Å2)
T33 (Å2)
Origin x (Å)
Origin y (Å)
Origin z (Å)
1
1.2232
0.1583
-0.4733
2.0983
1.0987
5.2952
0.1642
0.0429
-0.0761
0.1043
0.0967
-0.1662
-0.1968
-0.0153
-0.2609
-0.3218
-0.0514
-0.0444
-0.2158
0.0746
-0.2344
-29.7665
11.1629
7.5733
2
3.5112
-0.7345
-2.3777
1.6333
0.6863
3.0476
-0.3287
0.032
-0.0663
0.1474
0.111
-0.0806
0.2567
-0.0846
0.2177
-0.2683
-0.0158
-0.0505
-0.1781
0.0736
-0.3442
-33.6483
49.0702
14.7614
3
2.7396
-0.1592
0.4646
5.7321
1.2144
2.62
0.0659
0.2731
-0.1366
0.6344
-0.0211
-0.8488
0.4341
0.0176
-0.0448
-0.1684
-0.0596
-0.091
-0.1465
-0.0319
-0.2206
10.989
54.0714
32.7839
4
3.8049
1.5212
0.677
5.5385
-0.3992
1.9172
0.1132
0.1613
0.458
-0.2756
-0.0466
1.05
-0.1527
0.2328
-0.0666
-0.2361
-0.0652
-0.0847
-0.1694
-0.0049
-0.074
43.2799
66.7033
52.69
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Selection details
1
X-RAY DIFFRACTION
1
{ A|* }
2
X-RAY DIFFRACTION
2
{ B|* }
3
X-RAY DIFFRACTION
3
{ C|* }
4
X-RAY DIFFRACTION
4
{ D|* }
+
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