Evidence: SAXS, Theoretical and experimental curves match, and Radius of gyration agrees with the design model., mass spectrometry, Native mass spectrometry confirmed the presence of the heterodimer ...Evidence: SAXS, Theoretical and experimental curves match, and Radius of gyration agrees with the design model., mass spectrometry, Native mass spectrometry confirmed the presence of the heterodimer in solution., gel filtration, Protein eluted as a monodisperse peak at the expected volume.
Type
Name
Symmetry operation
Number
identity operation
1_555
x,y,z
1
Buried area
3370 Å2
ΔGint
-18 kcal/mol
Surface area
8560 Å2
Method
PISA
Unit cell
Length a, b, c (Å)
44.918, 48.755, 64.152
Angle α, β, γ (deg.)
90.00, 90.00, 90.00
Int Tables number
19
Space group name H-M
P212121
-
Components
#1: Protein
DHD127_A
Mass: 9119.329 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)
#2: Protein
DHD127_B
Mass: 9213.521 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)
Method to determine structure: MOLECULAR REPLACEMENT Starting model: Computational design model Resolution: 1.753→38.817 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.77 Details: Iterative rounds of manual model building in Coot and refinement with Phenix.
Rfactor
Num. reflection
% reflection
Rfree
0.2085
687
4.73 %
Rwork
0.1968
-
-
obs
0.1974
14512
98.94 %
Solvent computation
Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parameters
Biso mean: 21.1 Å2
Refinement step
Cycle: LAST / Resolution: 1.753→38.817 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
1241
0
0
149
1390
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
X-RAY DIFFRACTION
f_bond_d
0.011
1293
X-RAY DIFFRACTION
f_angle_d
1.157
1734
X-RAY DIFFRACTION
f_dihedral_angle_d
24.268
846
X-RAY DIFFRACTION
f_chiral_restr
0.073
197
X-RAY DIFFRACTION
f_plane_restr
0.008
232
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
1.7534-1.8888
0.3281
134
0.2613
2708
X-RAY DIFFRACTION
99
1.8888-2.0789
0.3192
115
0.2734
2667
X-RAY DIFFRACTION
97
2.0789-2.3797
0.231
119
0.1987
2772
X-RAY DIFFRACTION
99
2.3797-2.998
0.2009
161
0.1829
2774
X-RAY DIFFRACTION
100
2.998-38.8265
0.1713
158
0.1752
2904
X-RAY DIFFRACTION
100
+
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