Evidence: gel filtration, Indeed, as shown in size-exclusion chromatography, the elution volume of Sizzled on a Supedex 200 column was 16.2 ml, a volume corresponding to an eluted protein with an ...Evidence: gel filtration, Indeed, as shown in size-exclusion chromatography, the elution volume of Sizzled on a Supedex 200 column was 16.2 ml, a volume corresponding to an eluted protein with an apparent molecular weight of ~35 kD. As seen in the same figure, Sizzled migrated as a band on a SDS-PAGE gel, equivalent to a MW of ~ 33 kD. These results show that Sizzled exists as a monomer in the solution.
Type
Name
Symmetry operation
Number
identity operation
1_555
x,y,z
1
Buried area
220 Å2
ΔGint
-18 kcal/mol
Surface area
14450 Å2
Method
PISA
Unit cell
Length a, b, c (Å)
70.131, 70.131, 132.584
Angle α, β, γ (deg.)
90.00, 90.00, 90.00
Int Tables number
96
Space group name H-M
P43212
-
Components
#1: Protein
SecretedXwnt8inhibitorsizzled
Mass: 29757.486 Da / Num. of mol.: 1 / Fragment: UNP residues 24-281 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: szl / Cell line (production host): 293 GnTI / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: O73821
Method to determine structure: SAD / Resolution: 2.077→19.855 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 27.68 / Stereochemistry target values: ML
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.23
989
4.81 %
RANDOM
Rwork
0.2135
-
-
-
obs
0.2143
20553
99.48 %
-
Solvent computation
Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement step
Cycle: LAST / Resolution: 2.077→19.855 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
1968
0
19
107
2094
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
X-RAY DIFFRACTION
f_bond_d
0.002
2049
X-RAY DIFFRACTION
f_angle_d
0.457
2783
X-RAY DIFFRACTION
f_dihedral_angle_d
12.135
1262
X-RAY DIFFRACTION
f_chiral_restr
0.038
305
X-RAY DIFFRACTION
f_plane_restr
0.003
352
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
2.0768-2.1862
0.3194
163
0.277
2690
X-RAY DIFFRACTION
99
2.1862-2.323
0.3694
134
0.2823
2754
X-RAY DIFFRACTION
100
2.323-2.502
0.2845
135
0.2457
2778
X-RAY DIFFRACTION
100
2.502-2.7532
0.2702
113
0.2617
2778
X-RAY DIFFRACTION
100
2.7532-3.1503
0.2878
141
0.2418
2785
X-RAY DIFFRACTION
99
3.1503-3.9638
0.2074
134
0.2041
2828
X-RAY DIFFRACTION
99
3.9638-19.8555
0.192
169
0.1819
2951
X-RAY DIFFRACTION
99
+
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