ADP-ribosylation factor-like protein 8A/8B / small GTPase Arf family profile. / Sar1p-like members of the Ras-family of small GTPases / Small GTPase superfamily, ARF/SAR type / ADP-ribosylation factor family / ARF-like small GTPases; ARF, ADP-ribosylation factor / Rab subfamily of small GTPases / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold ...ADP-ribosylation factor-like protein 8A/8B / small GTPase Arf family profile. / Sar1p-like members of the Ras-family of small GTPases / Small GTPase superfamily, ARF/SAR type / ADP-ribosylation factor family / ARF-like small GTPases; ARF, ADP-ribosylation factor / Rab subfamily of small GTPases / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta Similarity search - Domain/homology
BIOMOLECULE: THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). ...BIOMOLECULE: THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). THE BIOLOGICAL MOLECULE FOR THE PROTEIN IS UNKNOWN.
ADP-ribosylationfactor-likeprotein8A / ADP-ribosylation factor-like protein 10B / Novel small G protein indispensable for equal chromosome ...ADP-ribosylation factor-like protein 10B / Novel small G protein indispensable for equal chromosome segregation 2
Mass: 22055.381 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ARL8A, ARL10B, GIE2 / Plasmid: p28a-LIC / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q96BM9
Resolution: 1.902→30 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.925 / WRfactor Rfree: 0.243 / WRfactor Rwork: 0.199 / SU B: 7.677 / SU ML: 0.114 / TLS residual ADP flag: LIKELY RESIDUAL / ESU R: 0.181 / ESU R Free: 0.16 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. arp/warp, molprobity were also used for the refinement
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.2414
693
5.079 %
random
Rwork
0.2013
-
-
-
all
0.203
-
-
-
obs
-
13645
95.426 %
-
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: 16.145 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-0.454 Å2
0 Å2
-0.285 Å2
2-
-
-0.511 Å2
0 Å2
3-
-
-
0.701 Å2
Refinement step
Cycle: LAST / Resolution: 1.902→30 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
1372
0
33
57
1462
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.016
0.022
1444
X-RAY DIFFRACTION
r_angle_refined_deg
1.375
1.994
1956
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
4.609
5
174
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
39.297
25.333
60
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
12.686
15
273
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
18.289
15
6
X-RAY DIFFRACTION
r_chiral_restr
0.09
0.2
222
X-RAY DIFFRACTION
r_gen_planes_refined
0.004
0.02
1035
X-RAY DIFFRACTION
r_nbd_refined
0.196
0.2
674
X-RAY DIFFRACTION
r_nbtor_refined
0.295
0.2
994
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.131
0.2
71
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.225
0.2
36
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.088
0.2
4
X-RAY DIFFRACTION
r_mcbond_it
2.024
2
906
X-RAY DIFFRACTION
r_mcangle_it
2.792
3
1400
X-RAY DIFFRACTION
r_scbond_it
2.27
2
653
X-RAY DIFFRACTION
r_scangle_it
3.07
3
555
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 (%)
1.902-1.951
0.287
52
0.224
931
0.227
1057
92.999
1.951-2.005
0.259
56
0.202
869
0.205
1001
92.408
2.005-2.062
0.266
44
0.204
899
0.207
1007
93.644
2.062-2.126
0.243
51
0.182
832
0.185
944
93.538
2.126-2.195
0.298
48
0.185
864
0.191
970
94.021
2.195-2.271
0.199
52
0.207
796
0.207
892
95.067
2.271-2.357
0.273
36
0.196
794
0.199
882
94.104
2.357-2.452
0.284
36
0.205
766
0.209
837
95.818
2.452-2.561
0.242
40
0.192
730
0.194
803
95.89
2.561-2.685
0.344
29
0.213
723
0.217
783
96.041
2.685-2.829
0.257
44
0.214
665
0.217
738
96.07
2.829-2.998
0.232
30
0.223
646
0.224
694
97.406
2.998-3.203
0.297
31
0.21
607
0.214
659
96.813
3.203-3.457
0.218
24
0.215
565
0.215
606
97.195
3.457-3.781
0.22
33
0.192
520
0.194
565
97.876
3.781-4.219
0.183
31
0.17
480
0.171
520
98.269
4.219-4.856
0.182
21
0.174
437
0.174
465
98.495
4.856-5.909
0.218
13
0.204
367
0.205
386
98.446
5.909-8.199
0.278
18
0.252
288
0.253
310
98.71
8.199-30
0.34
4
0.212
173
0.215
180
98.333
Refinement TLS params.
Method: refined / Refine-ID: X-RAY DIFFRACTION
ID
L11 (°2)
L12 (°2)
L13 (°2)
L22 (°2)
L23 (°2)
L33 (°2)
S11 (Å °)
S12 (Å °)
S13 (Å °)
S21 (Å °)
S22 (Å °)
S23 (Å °)
S31 (Å °)
S32 (Å °)
S33 (Å °)
T11 (Å2)
T12 (Å2)
T13 (Å2)
T22 (Å2)
T23 (Å2)
T33 (Å2)
Origin x (Å)
Origin y (Å)
Origin z (Å)
1
1.7838
1.0381
0.1478
5.8603
-0.481
2.7616
0.0193
0.0915
-0.0327
0.2438
0.0125
-0.1635
-0.0193
-0.2351
-0.0317
-0.1463
0.012
-0.0025
-0.0957
-0.0229
-0.1287
-18.3338
11.0293
50.1345
2
1.3314
-0.8663
2.2368
4.3521
-3.5092
4.8714
0.0204
-0.1473
-0.6661
-0.4021
-0.3757
-1.1057
0.4099
0.6012
0.3553
-0.0573
0.0286
0.0648
-0.0817
-0.0602
0.1438
-10.2304
1.8711
45.7456
Refinement TLS group
Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth asym-ID: A
ID
Refine TLS-ID
Label asym-ID
Auth seq-ID
Label seq-ID
1
1
A
3 - 181
14 - 192
2
2
B
201
+
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