DNA ligase (ATP or NAD+) / DNA ligation involved in DNA repair / DNA ligase (ATP) activity / DNA biosynthetic process / DNA recombination / DNA replication / cell cycle / cell division / DNA binding / ATP binding / metal ion binding Similarity search - Function
DNA ligase, ATP-dependent, bacterial/archaeal / DNA ligase i, domain 1 / DNA ligase, ATP-dependent, N-terminal domain / DNA ligase, ATP-dependent / DNA ligase, ATP-dependent, N-terminal / DNA ligase, ATP-dependent, N-terminal domain superfamily / DNA ligase N terminus / DNA ligase/mRNA capping enzyme / ATP-dependent DNA ligase signature 2. / ATP-dependent DNA ligase AMP-binding site. ...DNA ligase, ATP-dependent, bacterial/archaeal / DNA ligase i, domain 1 / DNA ligase, ATP-dependent, N-terminal domain / DNA ligase, ATP-dependent / DNA ligase, ATP-dependent, N-terminal / DNA ligase, ATP-dependent, N-terminal domain superfamily / DNA ligase N terminus / DNA ligase/mRNA capping enzyme / ATP-dependent DNA ligase signature 2. / ATP-dependent DNA ligase AMP-binding site. / DNA ligase, ATP-dependent, C-terminal / ATP dependent DNA ligase C terminal region / DNA ligase, ATP-dependent, conserved site / ATP-dependent DNA ligase family profile. / DNA ligase, ATP-dependent, central / ATP dependent DNA ligase domain / D-amino Acid Aminotransferase; Chain A, domain 1 / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta Similarity search - Domain/homology
Resolution: 2.85→29.295 Å / SU ML: 1.04 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 36.96 / Stereochemistry target values: ML Details: Relatively low number of observations did not allow to perform refinement of B-factors for each atom. One B-factor was refined for each residue
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.3575
797
5.12 %
Random
Rwork
0.2733
-
-
-
obs
0.2772
15576
98.95 %
-
all
-
49848
-
-
Solvent computation
Shrinkage radii: 1.11 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 65.716 Å2 / ksol: 0.276 e/Å3
Displacement parameters
Baniso -1
Baniso -2
Baniso -3
1-
31.4777 Å2
-0 Å2
-0 Å2
2-
-
-18.7236 Å2
-0 Å2
3-
-
-
-12.7541 Å2
Refinement step
Cycle: LAST / Resolution: 2.85→29.295 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
3859
0
23
2
3884
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
X-RAY DIFFRACTION
f_bond_d
0.01
3949
X-RAY DIFFRACTION
f_angle_d
1.5
5347
X-RAY DIFFRACTION
f_dihedral_angle_d
21.718
1439
X-RAY DIFFRACTION
f_chiral_restr
0.093
614
X-RAY DIFFRACTION
f_plane_restr
0.007
687
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
2.8501-3.0285
0.4524
129
0.3957
2424
X-RAY DIFFRACTION
100
3.0285-3.262
0.3762
144
0.3437
2419
X-RAY DIFFRACTION
100
3.262-3.5898
0.3875
134
0.304
2445
X-RAY DIFFRACTION
99
3.5898-4.108
0.3531
148
0.2784
2414
X-RAY DIFFRACTION
98
4.108-5.171
0.3853
130
0.2437
2454
X-RAY DIFFRACTION
98
5.171-29.2965
0.29
112
0.2413
2623
X-RAY DIFFRACTION
99
+
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