Evidence: mass spectrometry, Native Mass Spectrometry confirms the presence of the heterodimer in solution, gel filtration, Protein elutes as a monodisperse peak at the expected volume
Mass: 9529.052 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Protein
DHD15_extended_B
Mass: 9583.223 Da / Num. of mol.: 2 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: 2.25→43.023 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 33.46 Details: Iterative rounds of manual model building in Coot and refinement with Phenix Refine. Ultimately, resolution was trimmed to 2.25 from the high of the 1.83 diffraction data, as the high ...Details: Iterative rounds of manual model building in Coot and refinement with Phenix Refine. Ultimately, resolution was trimmed to 2.25 from the high of the 1.83 diffraction data, as the high resolution data, as evidenced by the refinement R-factors, was deemed too weak to be useful.
Rfactor
Num. reflection
% reflection
Rfree
0.3097
1033
7.3 %
Rwork
0.2609
-
-
obs
0.2645
14150
94.61 %
Solvent computation
Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parameters
Biso mean: 39.03 Å2
Refinement step
Cycle: LAST / Resolution: 2.25→43.023 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
2446
0
5
30
2481
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
X-RAY DIFFRACTION
f_bond_d
0.002
2454
X-RAY DIFFRACTION
f_angle_d
0.411
3267
X-RAY DIFFRACTION
f_dihedral_angle_d
16.034
1601
X-RAY DIFFRACTION
f_chiral_restr
0.025
385
X-RAY DIFFRACTION
f_plane_restr
0.001
422
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
2.2501-2.3687
0.3555
131
0.3171
1587
X-RAY DIFFRACTION
82
2.3687-2.5171
0.3552
134
0.3077
1821
X-RAY DIFFRACTION
93
2.5171-2.7114
0.3552
144
0.3125
1818
X-RAY DIFFRACTION
95
2.7114-2.9842
0.3591
148
0.2997
1887
X-RAY DIFFRACTION
96
2.9842-3.4159
0.3182
155
0.2789
1947
X-RAY DIFFRACTION
99
3.4159-4.303
0.2706
157
0.2194
1975
X-RAY DIFFRACTION
99
4.303-43.0304
0.2996
164
0.2462
2082
X-RAY DIFFRACTION
98
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
0.0434
0.288
-0.2242
0.1876
0.1674
0.6199
-0.0868
0.0735
0.0772
0.0172
-0.2282
0.06
-0.245
-0.141
-0.0371
0.4358
0.0569
-0.0072
0.4365
-0.0154
0.3831
12.9283
39.6853
61.239
2
0.1943
0.1146
0.4052
0.3321
0.4822
2.3622
-0.1008
-0.0713
-0.0776
0.0512
-0.2789
-0.026
0.8648
0.3402
-0.0395
0.4147
-0.001
0.0096
0.2884
0.0411
0.3583
16.8012
30.7311
62.1054
3
-0.1006
0.0125
-0.411
0.5706
0.1426
2.1778
-0.0907
-0.0255
-0.0387
0.1214
-0.2135
-0.0858
-0.5348
0.9171
0.0119
0.3365
-0.02
-0.0049
0.4925
0.0623
0.3703
19.953
36.2987
65.9131
4
0.1548
-0.0739
0.167
0.5115
0.0221
1.6562
0.0538
-0.0592
-0.0235
-0.1098
-0.185
0.0002
0.3064
-0.5664
0.003
0.3368
-0.0879
-0.0001
0.4689
-0.0355
0.3843
10.2214
33.828
65.1559
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Selection details
1
X-RAY DIFFRACTION
1
(chain 'D' andresid78through151)
2
X-RAY DIFFRACTION
2
(chain 'A' andresid0through77)
3
X-RAY DIFFRACTION
3
(chain 'B' andresid78through152)
4
X-RAY DIFFRACTION
4
(chain 'C' andresid0through77)
+
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