Mass: 9540.786 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Protein
DHD131_B
Mass: 9933.978 Da / Num. of mol.: 4 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: 2.38→42.99 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 31.78 Details: Iterative rounds of model building in Coot and refinement with Phenix.
Rfactor
Num. reflection
% reflection
Rfree
0.2832
1738
8.14 %
Rwork
0.2408
-
-
obs
0.2443
21356
87.2 %
Solvent computation
Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement step
Cycle: LAST / Resolution: 2.38→42.99 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
4622
0
0
63
4685
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
X-RAY DIFFRACTION
f_bond_d
0.002
4650
X-RAY DIFFRACTION
f_angle_d
0.446
6258
X-RAY DIFFRACTION
f_dihedral_angle_d
14.74
2933
X-RAY DIFFRACTION
f_chiral_restr
0.024
741
X-RAY DIFFRACTION
f_plane_restr
0.001
803
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
2.3801-2.4501
0.4456
121
0.344
1379
X-RAY DIFFRACTION
73
2.4501-2.5292
0.4013
122
0.325
1384
X-RAY DIFFRACTION
75
2.5292-2.6196
0.361
122
0.3314
1462
X-RAY DIFFRACTION
77
2.6196-2.7244
0.3851
126
0.3141
1450
X-RAY DIFFRACTION
79
2.7244-2.8484
0.3536
141
0.2846
1541
X-RAY DIFFRACTION
82
2.8484-2.9985
0.3121
147
0.2712
1578
X-RAY DIFFRACTION
85
2.9985-3.1863
0.298
154
0.2592
1659
X-RAY DIFFRACTION
90
3.1863-3.4323
0.2975
163
0.2442
1790
X-RAY DIFFRACTION
95
3.4323-3.7775
0.2751
151
0.2035
1815
X-RAY DIFFRACTION
96
3.7775-4.3237
0.23
161
0.1918
1836
X-RAY DIFFRACTION
97
4.3237-5.4456
0.2196
162
0.1994
1831
X-RAY DIFFRACTION
98
5.4456-42.9988
0.2466
168
0.2339
1893
X-RAY DIFFRACTION
98
+
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