A: IQ MOTIF AND SEC7 DOMAIN-CONTAINING PROTEIN 1 B: IQ MOTIF AND SEC7 DOMAIN-CONTAINING PROTEIN 1 C: ADP-RIBOSYLATION FACTOR 1 D: ADP-RIBOSYLATION FACTOR 1 E: IQ MOTIF AND SEC7 DOMAIN-CONTAINING PROTEIN 1 F: IQ MOTIF AND SEC7 DOMAIN-CONTAINING PROTEIN 1 G: ADP-RIBOSYLATION FACTOR 1 H: ADP-RIBOSYLATION FACTOR 1 hetero molecules
Mass: 523.180 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O14P3
Sequence details
ARF1 WAS DELETED FROM ITS 17 FIRST AMINO ACIDS IN THE STRUCTURE ISOFORM 2 AND IN THE STRUCTURE ...ARF1 WAS DELETED FROM ITS 17 FIRST AMINO ACIDS IN THE STRUCTURE ISOFORM 2 AND IN THE STRUCTURE SEQUENCE REMAINS A PART OF THE CLEAVED 6-HISTAG GAMGSGIP
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Experimental details
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Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
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Sample preparation
Crystal
Density Matthews: 2.32 Å3/Da / Density % sol: 46.99 % / Description: NONE
Crystal grow
pH: 6 Details: 0.15 M AMMONIUM SULFATE, 0.1 M MES PH 6 AND 16% PEG 4000
Resolution: 3.3→42.84 Å / Cor.coef. Fo:Fc: 0.9122 / Cor.coef. Fo:Fc free: 0.867 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.549 Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.2483
1757
5 %
RANDOM
Rwork
0.1988
-
-
-
obs
0.2013
35125
99.28 %
-
Displacement parameters
Biso mean: 69.56 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-11.5765 Å2
0 Å2
6.0514 Å2
2-
-
1.1759 Å2
0 Å2
3-
-
-
10.4006 Å2
Refine analyze
Luzzati coordinate error obs: 0.715 Å
Refinement step
Cycle: LAST / Resolution: 3.3→42.84 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
16794
0
128
0
16922
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
Restraint function
Weight
X-RAY DIFFRACTION
t_bond_d
0.01
17243
HARMONIC
2
X-RAY DIFFRACTION
t_angle_deg
1.32
23254
HARMONIC
2
X-RAY DIFFRACTION
t_dihedral_angle_d
6370
SINUSOIDAL
2
X-RAY DIFFRACTION
t_incorr_chiral_ct
X-RAY DIFFRACTION
t_pseud_angle
X-RAY DIFFRACTION
t_trig_c_planes
495
HARMONIC
2
X-RAY DIFFRACTION
t_gen_planes
2494
HARMONIC
5
X-RAY DIFFRACTION
t_it
17243
HARMONIC
20
X-RAY DIFFRACTION
t_nbd
X-RAY DIFFRACTION
t_omega_torsion
3.25
X-RAY DIFFRACTION
t_other_torsion
22.15
X-RAY DIFFRACTION
t_improper_torsion
X-RAY DIFFRACTION
t_chiral_improper_torsion
2171
SEMIHARMONIC
5
X-RAY DIFFRACTION
t_sum_occupancies
X-RAY DIFFRACTION
t_utility_distance
X-RAY DIFFRACTION
t_utility_angle
X-RAY DIFFRACTION
t_utility_torsion
X-RAY DIFFRACTION
t_ideal_dist_contact
20192
SEMIHARMONIC
4
LS refinement shell
Resolution: 3.3→3.4 Å / Total num. of bins used: 18
Rfactor
Num. reflection
% reflection
Rfree
0.254
132
5.02 %
Rwork
0.2184
2496
-
all
0.2203
2628
-
obs
-
-
99.28 %
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
1.1772
-1.3937
-0.6131
2.808
0.8912
2.4836
-0.0768
-0.0465
0.0636
0.1394
0.2202
-0.0608
0.1137
-0.1259
-0.1433
-0.1974
-0.033
0.0669
-0.0858
-0.0214
-0.151
-65.6304
-13.0234
-79.584
2
1.2837
1.3726
-0.2436
4.0736
-1.1709
1.7723
0.009
0.1357
-0.0214
-0.2457
-0.0793
0.0206
0.2712
0.0683
0.0703
-0.0252
0.0846
-0.0349
-0.1771
-0.0022
-0.2916
-14.9652
-13.7905
-21.0681
3
9.1464
-1.7467
1.8657
7.0486
0.2953
8.0708
-0.2952
0.4641
-0.1575
0.0176
-0.1036
0.098
-0.119
0.1679
0.3989
-0.341
-0.0654
-0.0629
-0.2537
-0.0125
-0.1788
14.4861
-28.1776
-38.0779
4
6.7807
0.8281
2.3526
5.7527
-1.2286
5.0991
-0.1724
-0.4059
0.4909
-0.0143
-0.1261
-0.0983
-0.1295
0.2714
0.2985
-0.2487
0.0797
0.0254
-0.0923
-0.0383
-0.2432
-10.4385
-30.2623
-54.9273
5
1.2175
-1.2543
-0.8746
3.0581
1.2584
2.7888
-0.0849
-0.0084
-0.0088
0.0017
0.0138
0.061
0.1976
-0.0377
0.071
-0.2129
-0.0802
-0.0105
-0.0813
0.0396
-0.1994
-22.8974
-46.0897
-75.4601
6
0.5379
0.8383
-0.2245
2.2419
-1.0791
1.9163
0.032
0.0574
-0.1111
0.1809
-0.0742
-0.2609
0.0099
0.1288
0.0422
-0.0317
0.0662
0.01
-0.1161
0.0084
-0.1212
29.4824
-46.5683
-20.7294
7
7.3325
0.0308
1.7614
7.7117
-2.2391
5.6048
-0.4864
0.6663
0.3965
-0.2596
0.3245
0.8965
0.1505
-0.3067
0.1618
-0.2836
-0.2692
-0.2268
-0.1806
0.2028
-0.1988
-28.8847
4.4235
-40.0151
8
12.8822
-0.8909
0.0502
3.1847
4.4094
4.7945
-0.067
-1.14
1.1508
0.1982
0.6242
-1.0735
0.0206
0.4215
-0.5573
-0.5597
0.2346
-0.2794
-0.2364
-0.2805
0.411
-53.0528
4.2422
-59.8144
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Selection details
1
X-RAY DIFFRACTION
1
CHAINA
2
X-RAY DIFFRACTION
2
CHAINB
3
X-RAY DIFFRACTION
3
CHAINC
4
X-RAY DIFFRACTION
4
CHAIND
5
X-RAY DIFFRACTION
5
CHAINE
6
X-RAY DIFFRACTION
6
CHAINF
7
X-RAY DIFFRACTION
7
CHAING
8
X-RAY DIFFRACTION
8
CHAINH
+
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