Histidinetriadnucleotide-bindingprotein1 / Adenosine 5'-monophosphoramidase / Protein kinase C inhibitor 1 / Protein kinase C-interacting ...Adenosine 5'-monophosphoramidase / Protein kinase C inhibitor 1 / Protein kinase C-interacting protein 1 / PKCI-1
Mass: 13823.931 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HINT1, HINT, PKCI1, PRKCNH1 / Plasmid: pSGA02 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P49773, Hydrolases
Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.58→19.101 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.947 / SU B: 1.78 / SU ML: 0.061 / Cross valid method: THROUGHOUT / ESU R: 0.079 / ESU R Free: 0.085 Details: Hydrogens have been added in their riding positions
Rfactor
Num. reflection
% reflection
Rfree
0.1913
1625
5.131 %
Rwork
0.1474
30046
-
all
0.15
-
-
obs
-
31671
99.912 %
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parameters
Biso mean: 10.824 Å2
Baniso -1
Baniso -2
Baniso -3
1-
1.397 Å2
0 Å2
-0.114 Å2
2-
-
-0.473 Å2
0 Å2
3-
-
-
-0.893 Å2
Refinement step
Cycle: LAST / Resolution: 1.58→19.101 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
1766
0
36
390
2192
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.01
0.012
1987
X-RAY DIFFRACTION
r_bond_other_d
0.001
0.016
1859
X-RAY DIFFRACTION
r_angle_refined_deg
1.54
1.652
2710
X-RAY DIFFRACTION
r_angle_other_deg
0.547
1.599
4327
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
6.217
5
257
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
7.088
5
11
X-RAY DIFFRACTION
r_dihedral_angle_other_2_deg
0.143
5
1
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
14.214
10
343
X-RAY DIFFRACTION
r_dihedral_angle_6_deg
15.953
10
83
X-RAY DIFFRACTION
r_chiral_restr
0.084
0.2
283
X-RAY DIFFRACTION
r_gen_planes_refined
0.009
0.02
2355
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
422
X-RAY DIFFRACTION
r_nbd_refined
0.244
0.2
407
X-RAY DIFFRACTION
r_symmetry_nbd_other
0.202
0.2
1788
X-RAY DIFFRACTION
r_nbtor_refined
0.175
0.2
973
X-RAY DIFFRACTION
r_symmetry_nbtor_other
0.082
0.2
1026
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.188
0.2
266
X-RAY DIFFRACTION
r_symmetry_nbd_refined
0.162
0.2
18
X-RAY DIFFRACTION
r_nbd_other
0.138
0.2
61
X-RAY DIFFRACTION
r_symmetry_xyhbond_nbd_refined
0.183
0.2
35
X-RAY DIFFRACTION
r_mcbond_it
1.091
1.026
989
X-RAY DIFFRACTION
r_mcbond_other
1.09
1.026
988
X-RAY DIFFRACTION
r_mcangle_it
1.705
1.84
1259
X-RAY DIFFRACTION
r_mcangle_other
1.704
1.84
1260
X-RAY DIFFRACTION
r_scbond_it
1.656
1.177
998
X-RAY DIFFRACTION
r_scbond_other
1.656
1.177
998
X-RAY DIFFRACTION
r_scangle_it
2.558
2.081
1451
X-RAY DIFFRACTION
r_scangle_other
2.558
2.08
1452
X-RAY DIFFRACTION
r_lrange_it
5.488
14.622
2470
X-RAY DIFFRACTION
r_lrange_other
4.783
11.286
2324
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
Fsc free
Fsc work
% reflection obs (%)
WRfactor Rwork
1.58-1.621
0.247
113
0.239
2187
0.24
2300
0.946
0.954
100
0.215
1.621-1.665
0.236
108
0.221
2141
0.222
2249
0.958
0.962
100
0.193
1.665-1.713
0.245
116
0.207
2083
0.209
2199
0.953
0.969
100
0.177
1.713-1.765
0.229
140
0.186
2030
0.189
2170
0.964
0.975
100
0.153
1.765-1.822
0.2
125
0.175
1911
0.176
2036
0.967
0.978
100
0.144
1.822-1.886
0.243
112
0.169
1894
0.173
2006
0.962
0.981
100
0.14
1.886-1.956
0.178
73
0.152
1845
0.153
1918
0.981
0.984
100
0.127
1.956-2.035
0.177
82
0.139
1786
0.141
1868
0.98
0.988
100
0.119
2.035-2.125
0.209
82
0.147
1699
0.15
1782
0.972
0.987
99.9439
0.126
2.125-2.227
0.174
87
0.133
1640
0.135
1727
0.982
0.989
100
0.114
2.227-2.346
0.168
69
0.124
1560
0.126
1629
0.98
0.99
100
0.106
2.346-2.485
0.165
62
0.124
1481
0.126
1543
0.982
0.99
100
0.106
2.485-2.654
0.153
69
0.121
1392
0.123
1461
0.984
0.991
100
0.105
2.654-2.862
0.176
71
0.13
1302
0.132
1373
0.979
0.99
100
0.113
2.862-3.128
0.178
72
0.128
1173
0.131
1245
0.982
0.99
100
0.114
3.128-3.486
0.151
73
0.121
1079
0.123
1152
0.986
0.992
100
0.113
3.486-4.003
0.185
51
0.125
965
0.128
1016
0.982
0.991
100
0.119
4.003-4.849
0.16
34
0.116
833
0.117
867
0.985
0.992
100
0.111
4.849-6.647
0.257
63
0.169
641
0.177
704
0.976
0.987
100
0.162
6.647-19.101
0.169
23
0.181
404
0.18
430
0.984
0.981
99.3023
0.171
+
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