BIOMOLECULE: 1 SEE REMARK 350 FOR THE PROGRAM GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN ... BIOMOLECULE: 1 SEE REMARK 350 FOR THE PROGRAM GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN THIS ENTRY. AUTHORS STATE THAT THE BIOLOGICAL UNIT OF THIS POLYPEPTIDE IS UNKNOWN.
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: 0.97931 Å / Relative weight: 1
Reflection
Resolution: 1.9→50 Å / Num. obs: 19430 / % possible obs: 99.6 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.122 / Χ2: 1.512 / Net I/σ(I): 6.4
Reflection shell
Resolution (Å)
Redundancy (%)
Rmerge(I) obs
Num. unique all
Χ2
% possible all
1.9-1.97
5.4
0.709
1857
1.951
96.6
1.97-2.05
6.5
0.57
1894
0.834
99.7
2.05-2.14
6.8
0.468
1919
1.745
99.7
2.14-2.25
7.1
0.344
1928
1.233
99.8
2.25-2.39
7.3
0.266
1939
1.228
100
2.39-2.58
7.3
0.175
1923
1.004
100
2.58-2.84
7.3
0.127
1959
0.956
100
2.84-3.25
7.3
0.085
1948
1.206
100
3.25-4.09
7.2
0.07
1976
1.991
100
4.09-50
6.8
0.061
2087
3.032
99.8
-
Phasing
Phasing
Method: SAD
-
Processing
Software
Name
Version
Classification
NB
DENZO
datareduction
SCALEPACK
datascaling
SHELX
phasing
REFMAC
refmac_5.2.0019
refinement
PDB_EXTRACT
2
dataextraction
ADSC
Quantum
datacollection
HKL-2000
datareduction
Refinement
Method to determine structure: SAD / Resolution: 1.95→28.51 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.894 / WRfactor Rfree: 0.234 / WRfactor Rwork: 0.197 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.167 / ESU R Free: 0.159 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. Coot, arp/warp, molprobity programs have also been used in refinement
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.263
933
5.2 %
RANDOM
Rwork
0.219
-
-
-
all
0.222
-
-
-
obs
0.222
17990
99.78 %
-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parameters
Biso mean: 18.786 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0.25 Å2
0 Å2
0 Å2
2-
-
-0.04 Å2
0 Å2
3-
-
-
-0.21 Å2
Refinement step
Cycle: LAST / Resolution: 1.95→28.51 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
1480
0
33
66
1579
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.016
0.022
1550
X-RAY DIFFRACTION
r_bond_other_d
0
0.02
1038
X-RAY DIFFRACTION
r_angle_refined_deg
1.46
1.982
2116
X-RAY DIFFRACTION
r_angle_other_deg
4.148
3
2537
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.479
5
186
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
30.986
24.366
71
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
13.731
15
263
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
17.76
15
7
X-RAY DIFFRACTION
r_chiral_restr
0.082
0.2
232
X-RAY DIFFRACTION
r_gen_planes_refined
0.006
0.02
1688
X-RAY DIFFRACTION
r_gen_planes_other
0.008
0.02
318
X-RAY DIFFRACTION
r_nbd_refined
0.203
0.2
289
X-RAY DIFFRACTION
r_nbd_other
0.229
0.2
941
X-RAY DIFFRACTION
r_nbtor_refined
0.181
0.2
713
X-RAY DIFFRACTION
r_nbtor_other
0.108
0.2
652
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.149
0.2
64
X-RAY DIFFRACTION
r_metal_ion_refined
0
0.2
1
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.149
0.2
8
X-RAY DIFFRACTION
r_symmetry_vdw_other
0.21
0.2
35
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.162
0.2
14
X-RAY DIFFRACTION
r_mcbond_it
2.531
2
912
X-RAY DIFFRACTION
r_mcbond_other
0
2
362
X-RAY DIFFRACTION
r_mcangle_it
3.562
3
1490
X-RAY DIFFRACTION
r_scbond_it
2.604
2
638
X-RAY DIFFRACTION
r_scangle_it
3.409
3
622
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
Num. reflection all
% reflection obs (%)
1.95-2
0.418
74
0.33
1226
1315
98.859
2-2.055
0.321
50
0.297
1215
1271
99.528
2.055-2.114
0.326
69
0.268
1157
1230
99.675
2.114-2.179
0.264
66
0.239
1147
1214
99.918
2.179-2.25
0.29
60
0.267
1090
1157
99.395
2.25-2.328
0.319
61
0.249
1067
1130
99.823
2.328-2.416
0.321
50
0.199
1039
1089
100
2.416-2.514
0.254
62
0.205
1012
1074
100
2.514-2.624
0.271
61
0.217
948
1009
100
2.624-2.751
0.284
52
0.22
915
967
100
2.751-2.899
0.244
46
0.219
892
938
100
2.899-3.073
0.219
57
0.209
825
882
100
3.073-3.282
0.232
45
0.202
785
830
100
3.282-3.541
0.262
40
0.208
732
772
100
3.541-3.873
0.202
39
0.194
686
725
100
3.873-4.32
0.258
30
0.167
629
659
100
4.32-4.97
0.173
28
0.161
559
587
100
4.97-6.041
0.27
18
0.223
489
507
100
6.041-8.357
0.245
17
0.287
393
410
100
8.357-28.513
0.502
8
0.254
251
263
98.479
+
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