bidirectional double-stranded viral DNA replication / Hydrolases; Acting on ester bonds; Exodeoxyribonucleases producing 5'-phosphomonoesters / 3'-5' exonuclease activity / DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / nucleotide binding / DNA binding / metal ion binding Similarity search - Function
DnaQ-like 3'-5' exonuclease / Monooxygenase - #300 / Ribonuclease H-like motif / DNA-directed DNA polymerase T4 type / DNA Polymerase; Chain A, domain 1 / DNA Polymerase, chain B, domain 1 / B family DNA polymerase, finger domain / Palm domain of DNA polymerase / B family DNA polymerase, palm domain / Monooxygenase ...DnaQ-like 3'-5' exonuclease / Monooxygenase - #300 / Ribonuclease H-like motif / DNA-directed DNA polymerase T4 type / DNA Polymerase; Chain A, domain 1 / DNA Polymerase, chain B, domain 1 / B family DNA polymerase, finger domain / Palm domain of DNA polymerase / B family DNA polymerase, palm domain / Monooxygenase / DNA polymerase family B signature. / DNA-directed DNA polymerase, family B, conserved site / DNA polymerase family B / DNA polymerase family B, exonuclease domain / DNA-directed DNA polymerase, family B, exonuclease domain / DNA-directed DNA polymerase, family B, multifunctional domain / DNA polymerase, palm domain superfamily / DNA polymerase type-B family / DNA-directed DNA polymerase, family B / Ribonuclease H-like superfamily/Ribonuclease H / Helix Hairpins / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily / Ribonuclease H-like superfamily / DNA/RNA polymerase superfamily / Alpha-Beta Complex / Up-down Bundle / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta Similarity search - Domain/homology
Resolution: 2.28→46.2 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.941 / SU B: 16.939 / SU ML: 0.198 / Cross valid method: THROUGHOUT / ESU R: 0.296 / ESU R Free: 0.23 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.24911
2800
5.1 %
RANDOM
Rwork
0.19587
-
-
-
obs
0.19849
52490
98.09 %
-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parameters
Biso mean: 63.085 Å2
Baniso -1
Baniso -2
Baniso -3
1-
1.68 Å2
-0 Å2
0 Å2
2-
-
-0.54 Å2
0 Å2
3-
-
-
-1.14 Å2
Refinement step
Cycle: LAST / Resolution: 2.28→46.2 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
7363
612
37
187
8199
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.006
0.019
8269
X-RAY DIFFRACTION
r_bond_other_d
X-RAY DIFFRACTION
r_angle_refined_deg
1.114
1.907
11309
X-RAY DIFFRACTION
r_angle_other_deg
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.19
5
903
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
34.678
24.133
375
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
14.986
15
1350
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
15.688
15
47
X-RAY DIFFRACTION
r_chiral_restr
0.077
0.2
1168
X-RAY DIFFRACTION
r_gen_planes_refined
0.004
0.021
6107
X-RAY DIFFRACTION
r_gen_planes_other
X-RAY DIFFRACTION
r_nbd_refined
X-RAY DIFFRACTION
r_nbd_other
X-RAY DIFFRACTION
r_nbtor_refined
X-RAY DIFFRACTION
r_nbtor_other
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
X-RAY DIFFRACTION
r_xyhbond_nbd_other
X-RAY DIFFRACTION
r_metal_ion_refined
X-RAY DIFFRACTION
r_metal_ion_other
X-RAY DIFFRACTION
r_symmetry_vdw_refined
X-RAY DIFFRACTION
r_symmetry_vdw_other
X-RAY DIFFRACTION
r_symmetry_hbond_refined
X-RAY DIFFRACTION
r_symmetry_hbond_other
X-RAY DIFFRACTION
r_symmetry_metal_ion_refined
X-RAY DIFFRACTION
r_symmetry_metal_ion_other
X-RAY DIFFRACTION
r_mcbond_it
1.229
4
4504
X-RAY DIFFRACTION
r_mcbond_other
X-RAY DIFFRACTION
r_mcangle_it
2.175
6
7303
X-RAY DIFFRACTION
r_scbond_it
2.396
6
3766
X-RAY DIFFRACTION
r_scangle_it
3.586
9
4007
X-RAY DIFFRACTION
r_rigid_bond_restr
X-RAY DIFFRACTION
r_sphericity_free
X-RAY DIFFRACTION
r_sphericity_bonded
LS refinement shell
Resolution: 2.28→2.341 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.328
155
-
Rwork
0.267
2932
-
obs
-
-
78.49 %
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
0.8576
-0.2231
-0.3869
1.2533
0.0409
0.1899
-0.3244
0.2306
-0.3824
0.0733
0.1735
0.3373
0.0895
-0.0945
0.1508
0.1838
-0.113
-0.0243
0.5234
-0.0175
0.8199
-17.334
3.784
36.225
2
0.8406
-0.4232
0.1192
4.2491
-0.9771
1.0192
0.1416
0.0196
0.069
-0.214
-0.1163
-0.5556
0.1198
0.1903
-0.0254
0.0341
0.0185
0.0176
0.2599
-0.0059
0.6188
24.811
-0.193
32.18
3
0.8348
-0.6561
0.3755
2.1302
0.1966
1.6198
0.1026
0.1636
-0.0204
-0.4369
-0.1721
-0.1818
-0.0276
-0.0598
0.0695
0.1638
0.0321
0.1036
0.2924
0.023
0.4543
8.877
23.785
13.779
4
1.3524
-0.7137
-0.27
1.8868
0.6026
1.0677
-0.0844
-0.4041
-0.089
0.2724
0.1271
-0.0438
0.0934
-0.0933
-0.0427
0.0845
-0.0041
-0.039
0.3645
0.0592
0.362
-2.324
9.25
60.586
5
0.7779
-0.5638
-0.2303
5.8284
1.3464
1.7154
0.0989
-0.1295
0.1865
-0.2723
-0.0624
-0.3804
-0.4015
0.0778
-0.0365
0.1062
-0.0593
-0.0333
0.2964
-0.0089
0.5217
9.568
28.279
46.216
6
1.9106
-0.0025
0.3141
0.7476
0.5649
2.3226
-0.0932
-0.1786
0.0241
-0.0757
0.0282
-0.0885
-0.2104
-0.0376
0.065
0.1026
0.0254
-0.026
0.3458
0.0405
0.4664
-9.141
24.838
47.942
7
1.9429
-0.3506
-0.6705
1.6533
1.071
2.8272
-0.0434
0.2851
-0.0093
-0.3208
-0.1141
0.243
-0.1775
-0.422
0.1575
0.0727
0.029
-0.0768
0.377
0.014
0.449
-22.93
21.745
28.403
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Auth asym-ID
Auth seq-ID
1
X-RAY DIFFRACTION
1
T
2 - 18
2
X-RAY DIFFRACTION
1
P
103 - 114
3
X-RAY DIFFRACTION
1
P
115
4
X-RAY DIFFRACTION
1
A
1001
5
X-RAY DIFFRACTION
2
A
1 - 105
6
X-RAY DIFFRACTION
2
A
340 - 389
7
X-RAY DIFFRACTION
3
A
106 - 339
8
X-RAY DIFFRACTION
4
A
390 - 468
9
X-RAY DIFFRACTION
4
A
576 - 706
10
X-RAY DIFFRACTION
5
A
469 - 575
11
X-RAY DIFFRACTION
6
A
707 - 737
12
X-RAY DIFFRACTION
7
A
738 - 901
+
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