BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 ... BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). AUTHORS STATE THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS UNKNOWN. THE BIOLOGICAL UNIT ASSEMBLY SHOWN IN REMARK 350 IS PREDICTED BY THE ANALYSIS OF PROTEIN INTERFACES BASED ON THIS CRYSTAL STRUCTURE.
Mass: 24373.371 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NRK1, C9orf95 / Plasmid: p28a-LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) codon plus RIL References: UniProt: Q9NWW6, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 1.5418 Å / Relative weight: 1
Reflection
Resolution: 1.8→20 Å / Num. obs: 43446 / % possible obs: 98.9 % / Redundancy: 7.5 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 11
Reflection shell
Resolution (Å)
Redundancy (%)
Rmerge(I) obs
1.8-1.86
7.1
0.526
1.86-1.94
7.3
0.38
1.94-2.03
7.3
0.291
2.03-2.13
7.4
0.214
2.13-2.27
7.4
0.179
2.27-2.44
7.5
0.146
2.44-2.69
7.5
0.112
2.69-3.07
7.6
0.077
3.07-3.87
7.7
0.045
3.87-20
7.7
0.034
-
Phasing
Phasing
Method: molecular replacement
-
Processing
Software
Name
Version
Classification
NB
DENZO
datareduction
SCALEPACK
datascaling
REFMAC
refmac_5.2.0019
refinement
PDB_EXTRACT
1.701
dataextraction
Refinement
Method to determine structure: MOLECULAR REPLACEMENT Starting model: same protein in complex with nicotinamide mononucleotide based on an isomorphous crystal Resolution: 1.8→19.838 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.936 / SU B: 2.185 / SU ML: 0.07 / ESU R: 0.112 / ESU R Free: 0.11 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. Molprobity, prodrg, coot programs have also been used in the refinement
Rfactor
Num. reflection
% reflection
Rfree
0.2092
1181
5.167 %
Rwork
0.1745
-
-
all
0.176
-
-
obs
-
22855
98.897 %
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK BULK SOLVENT
Displacement parameters
Biso mean: 14.171 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0.289 Å2
0 Å2
0 Å2
2-
-
0.124 Å2
0 Å2
3-
-
-
-0.413 Å2
Refinement step
Cycle: LAST / Resolution: 1.8→19.838 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
1581
0
24
166
1771
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.017
0.022
1648
X-RAY DIFFRACTION
r_bond_other_d
0.002
0.02
1115
X-RAY DIFFRACTION
r_angle_refined_deg
1.45
1.977
2249
X-RAY DIFFRACTION
r_angle_other_deg
0.934
3.002
2719
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.477
5
202
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
31.513
24.75
80
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
12.111
15
286
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
16.152
15
8
X-RAY DIFFRACTION
r_chiral_restr
0.09
0.2
246
X-RAY DIFFRACTION
r_gen_planes_refined
0.006
0.02
1815
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
330
X-RAY DIFFRACTION
r_nbd_refined
0.209
0.2
288
X-RAY DIFFRACTION
r_nbd_other
0.186
0.2
1111
X-RAY DIFFRACTION
r_nbtor_refined
0.179
0.2
770
X-RAY DIFFRACTION
r_nbtor_other
0.084
0.2
767
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.138
0.2
117
X-RAY DIFFRACTION
r_xyhbond_nbd_other
X-RAY DIFFRACTION
r_metal_ion_refined
0.071
0.2
1
X-RAY DIFFRACTION
r_metal_ion_other
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.214
0.2
10
X-RAY DIFFRACTION
r_symmetry_vdw_other
0.159
0.2
38
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.164
0.2
20
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
2.441
2
1085
X-RAY DIFFRACTION
r_mcbond_other
0.685
2
385
X-RAY DIFFRACTION
r_mcangle_it
3.109
3
1593
X-RAY DIFFRACTION
r_scbond_it
2.526
2
763
X-RAY DIFFRACTION
r_scangle_it
3.571
3
649
X-RAY DIFFRACTION
r_rigid_bond_restr
X-RAY DIFFRACTION
r_sphericity_free
X-RAY DIFFRACTION
r_sphericity_bonded
LS refinement shell
Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Rfactor all
Num. reflection all
% reflection obs (%)
1.8-1.846
0.282
80
0.241
1561
0.243
1688
97.216
1.846-1.897
0.262
75
0.209
1494
0.212
1605
97.757
1.897-1.951
0.244
95
0.182
1476
0.186
1600
98.188
1.951-2.01
0.279
75
0.168
1414
0.173
1523
97.768
2.01-2.076
0.225
70
0.161
1413
0.164
1510
98.212
2.076-2.148
0.201
75
0.175
1355
0.176
1455
98.282
2.148-2.228
0.194
71
0.166
1321
0.167
1408
98.864
2.228-2.317
0.28
75
0.163
1258
0.169
1346
99.034
2.317-2.419
0.206
66
0.161
1223
0.164
1297
99.383
2.419-2.535
0.214
66
0.161
1180
0.164
1254
99.362
2.535-2.67
0.233
70
0.173
1111
0.176
1184
99.747
2.67-2.829
0.234
60
0.179
1060
0.182
1123
99.733
2.829-3.02
0.188
61
0.185
997
0.185
1059
99.906
3.02-3.255
0.191
60
0.186
942
0.186
1003
99.9
3.255-3.556
0.2
43
0.176
875
0.178
919
99.891
3.556-3.96
0.162
46
0.153
806
0.154
853
99.883
3.96-4.543
0.157
34
0.144
723
0.145
757
100
4.543-5.492
0.129
28
0.167
625
0.166
653
100
5.492-7.486
0.22
18
0.22
506
0.22
524
100
7.486-19.838
0.286
13
0.211
334
0.213
349
99.427
+
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