ethanolamine kinase / choline kinase / ethanolamine kinase activity / CDP-choline pathway / choline kinase activity / Synthesis of PE / phosphatidylethanolamine biosynthetic process / muscle organ development / Synthesis of PC / phosphorylation ...ethanolamine kinase / choline kinase / ethanolamine kinase activity / CDP-choline pathway / choline kinase activity / Synthesis of PE / phosphatidylethanolamine biosynthetic process / muscle organ development / Synthesis of PC / phosphorylation / ATP binding / cytosol / cytoplasm Similarity search - Function
Resolution: 1.42→30 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.952 / WRfactor Rfree: 0.216 / WRfactor Rwork: 0.186 / SU B: 1.095 / SU ML: 0.043 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.064 / ESU R Free: 0.066 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY. The program coot, as well as the PRODRG and MOLPROBITY servers were also used during refinement.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.213
3705
5.045 %
RANDOM
Rwork
0.187
-
-
-
obs
0.188
73434
99.876 %
-
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: 13.708 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-0.05 Å2
0 Å2
-0.037 Å2
2-
-
0.067 Å2
0 Å2
3-
-
-
-0.052 Å2
Refinement step
Cycle: LAST / Resolution: 1.42→30 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
2753
0
92
273
3118
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.018
0.022
3057
X-RAY DIFFRACTION
r_bond_other_d
0.001
0.02
2098
X-RAY DIFFRACTION
r_angle_refined_deg
1.498
2.001
4191
X-RAY DIFFRACTION
r_angle_other_deg
0.876
3.001
5067
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.465
5
373
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
32.055
23.557
149
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
11.82
15
497
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
15.699
15
20
X-RAY DIFFRACTION
r_chiral_restr
0.085
0.2
430
X-RAY DIFFRACTION
r_gen_planes_refined
0.008
0.021
3377
X-RAY DIFFRACTION
r_gen_planes_other
0.002
0.02
658
X-RAY DIFFRACTION
r_mcbond_it
0.875
1.5
1756
X-RAY DIFFRACTION
r_mcbond_other
0.245
1.5
697
X-RAY DIFFRACTION
r_mcangle_it
1.54
2
2846
X-RAY DIFFRACTION
r_scbond_it
2.226
3
1301
X-RAY DIFFRACTION
r_scangle_it
3.476
4.5
1328
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 (%)
1.42-1.457
0.304
285
0.301
5124
5422
99.76
1.457-1.497
0.29
267
0.267
5006
5274
99.981
1.497-1.54
0.249
222
0.234
4867
5090
99.98
1.54-1.587
0.242
258
0.201
4717
4975
100
1.587-1.639
0.222
260
0.195
4587
4847
100
1.639-1.696
0.216
242
0.179
4439
4681
100
1.696-1.76
0.205
220
0.182
4293
4513
100
1.76-1.832
0.206
257
0.171
4086
4343
100
1.832-1.913
0.185
182
0.172
4006
4188
100
1.913-2.006
0.211
191
0.179
3770
3962
99.975
2.006-2.114
0.207
177
0.18
3613
3791
99.974
2.114-2.241
0.194
200
0.17
3391
3597
99.833
2.241-2.395
0.192
170
0.171
3212
3384
99.941
2.395-2.586
0.244
149
0.179
2987
3137
99.968
2.586-2.831
0.205
150
0.186
2761
2911
100
2.831-3.161
0.209
137
0.198
2500
2637
100
3.161-3.643
0.219
110
0.19
2217
2334
99.7
3.643-4.446
0.171
90
0.155
1877
1973
99.696
4.446-6.219
0.187
82
0.178
1470
1557
99.679
6.219-30
0.282
56
0.226
806
909
94.829
+
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