Evidence: SAXS, Evidence for 2:1 complex at high concentration
Type
Name
Symmetry operation
Number
identity operation
1_555
x,y,z
1
Unit cell
Length a, b, c (Å)
75.160, 75.160, 273.770
Angle α, β, γ (deg.)
90.00, 90.00, 120.00
Int Tables number
179
Space group name H-M
P6522
-
Components
#1: Protein
Tribbleshomolog2 / TRB-2
Mass: 29987.256 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TRIB2, TRB2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q92519
#2: Antibody
Nb4.103Nanobody
Mass: 13004.367 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
Resolution: 2.7→45.67 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.879 / SU B: 14.451 / SU ML: 0.277 / Cross valid method: THROUGHOUT / ESU R Free: 0.384 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.25967
1021
8.4 %
RANDOM
Rwork
0.20187
-
-
-
obs
0.20676
11150
90.59 %
-
Solvent computation
Ion probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parameters
Biso mean: 58.447 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-0.25 Å2
-0.13 Å2
-0 Å2
2-
-
-0.25 Å2
0 Å2
3-
-
-
0.82 Å2
Refinement step
Cycle: LAST / Resolution: 2.7→45.67 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
2914
0
0
40
2954
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.004
0.017
2977
X-RAY DIFFRACTION
r_bond_other_d
0.001
0.019
2758
X-RAY DIFFRACTION
r_angle_refined_deg
0.955
1.864
4018
X-RAY DIFFRACTION
r_angle_other_deg
0.902
2.681
6352
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
4.889
5
365
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
28.472
21.25
160
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
12.164
15
506
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
10.467
15
22
X-RAY DIFFRACTION
r_chiral_restr
0.051
0.2
436
X-RAY DIFFRACTION
r_gen_planes_refined
0.002
0.02
3358
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
714
X-RAY DIFFRACTION
r_mcbond_it
5.375
5.81
1472
X-RAY DIFFRACTION
r_mcbond_other
5.354
5.808
1471
X-RAY DIFFRACTION
r_mcangle_it
8.391
8.691
1833
X-RAY DIFFRACTION
r_mcangle_other
8.39
8.695
1834
X-RAY DIFFRACTION
r_scbond_it
5.626
6.192
1505
X-RAY DIFFRACTION
r_scbond_other
5.624
6.192
1505
X-RAY DIFFRACTION
r_scangle_other
8.863
9.098
2186
X-RAY DIFFRACTION
r_long_range_B_refined
12.69
65.673
3200
X-RAY DIFFRACTION
r_long_range_B_other
12.697
65.715
3195
LS refinement shell
Resolution: 2.701→2.771 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.325
9
-
Rwork
0.265
135
-
obs
-
-
14.86 %
+
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