A: CD-NTase-associated protein 12 B: CD-NTase-associated protein 12 C: CD-NTase-associated protein 12 D: CD-NTase-associated protein 12 hetero molecules
Mass: 18813.592 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: The GLY4 should be re-indexed as GLY151. / Source: (gene. exp.) Epilithonimonas lactis (bacteria) / Gene: IO89_10965 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A085BE66
Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.553→25.769 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.915 / Cross valid method: THROUGHOUT / ESU R Free: 0.33 Details: Hydrogens have been added in their riding positions
Rfactor
Num. reflection
% reflection
Rfree
0.2276
962
4.912 %
Rwork
0.195
18622
-
all
0.197
-
-
obs
-
19584
89.818 %
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parameters
Biso mean: 45.432 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0.439 Å2
0 Å2
0.571 Å2
2-
-
-0.735 Å2
-0 Å2
3-
-
-
-0.164 Å2
Refinement step
Cycle: LAST / Resolution: 2.553→25.769 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
5151
0
88
172
5411
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.008
0.013
5337
X-RAY DIFFRACTION
r_bond_other_d
0.034
0.017
5139
X-RAY DIFFRACTION
r_angle_refined_deg
1.438
1.649
7231
X-RAY DIFFRACTION
r_angle_other_deg
2.272
1.583
11858
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
6.597
5
636
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
37.829
24.323
266
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
18.753
15
983
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
18.662
15
20
X-RAY DIFFRACTION
r_chiral_restr
0.079
0.2
735
X-RAY DIFFRACTION
r_gen_planes_refined
0.007
0.02
5942
X-RAY DIFFRACTION
r_gen_planes_other
0.008
0.02
1154
X-RAY DIFFRACTION
r_nbd_refined
0.209
0.2
1099
X-RAY DIFFRACTION
r_symmetry_nbd_other
0.231
0.2
4810
X-RAY DIFFRACTION
r_nbtor_refined
0.172
0.2
2544
X-RAY DIFFRACTION
r_symmetry_nbtor_other
0.072
0.2
2558
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.165
0.2
147
X-RAY DIFFRACTION
r_symmetry_xyhbond_nbd_other
0.124
0.2
8
X-RAY DIFFRACTION
r_symmetry_nbd_refined
0.217
0.2
28
X-RAY DIFFRACTION
r_nbd_other
0.288
0.2
106
X-RAY DIFFRACTION
r_symmetry_xyhbond_nbd_refined
0.146
0.2
6
X-RAY DIFFRACTION
r_mcbond_it
3.972
4.653
2559
X-RAY DIFFRACTION
r_mcbond_other
3.972
4.653
2558
X-RAY DIFFRACTION
r_mcangle_it
6.585
6.965
3190
X-RAY DIFFRACTION
r_mcangle_other
6.584
6.965
3191
X-RAY DIFFRACTION
r_scbond_it
3.881
4.956
2778
X-RAY DIFFRACTION
r_scbond_other
3.878
4.956
2775
X-RAY DIFFRACTION
r_scangle_it
6.455
7.209
4041
X-RAY DIFFRACTION
r_scangle_other
6.452
7.209
4040
X-RAY DIFFRACTION
r_lrange_it
10.577
53.542
5824
X-RAY DIFFRACTION
r_lrange_other
10.578
53.544
5824
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
2.553-2.619
0.27
51
0.234
869
X-RAY DIFFRACTION
57.7164
2.619-2.69
0.199
47
0.211
1001
X-RAY DIFFRACTION
68.5415
2.69-2.767
0.283
52
0.227
1139
X-RAY DIFFRACTION
77.5896
2.767-2.852
0.266
58
0.24
1154
X-RAY DIFFRACTION
83.9335
2.852-2.944
0.269
60
0.233
1258
X-RAY DIFFRACTION
92.1678
2.944-3.047
0.277
66
0.232
1220
X-RAY DIFFRACTION
95.4006
3.047-3.16
0.204
63
0.225
1215
X-RAY DIFFRACTION
96.6717
3.16-3.288
0.239
67
0.221
1164
X-RAY DIFFRACTION
94.1131
3.288-3.432
0.241
72
0.212
1127
X-RAY DIFFRACTION
98.8458
3.432-3.597
0.229
55
0.2
1097
X-RAY DIFFRACTION
98.2097
3.597-3.789
0.26
58
0.194
1049
X-RAY DIFFRACTION
98.5752
3.789-4.015
0.214
54
0.178
1000
X-RAY DIFFRACTION
98.8743
4.015-4.287
0.205
45
0.158
952
X-RAY DIFFRACTION
98.8107
4.287-4.622
0.149
43
0.153
868
X-RAY DIFFRACTION
97.3291
4.622-5.051
0.206
31
0.152
807
X-RAY DIFFRACTION
97.783
5.051-5.628
0.263
39
0.197
722
X-RAY DIFFRACTION
96.9427
5.628-6.461
0.291
30
0.231
677
X-RAY DIFFRACTION
99.2978
6.461-7.822
0.204
37
0.193
558
X-RAY DIFFRACTION
99.3322
7.822-10.705
0.169
27
0.146
461
X-RAY DIFFRACTION
98.9858
10.705-25.769
0.332
7
0.203
284
X-RAY DIFFRACTION
93.5691
+
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