Mass: 18.015 Da / Num. of mol.: 504 / Source method: isolated from a natural source / Formula: H2O
-
Experimental details
-
Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
-
Sample preparation
Crystal
Density Matthews: 2.46 Å3/Da / Density % sol: 49.99 %
Crystal grow
Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8.8 Details: 100 mM Tris (pH 8.8), 50 mM MgCl2, 25% (v/v) pentaerythritol propoxylate (17/8 PO/OH), 10 mM AMPNP, 10 mM magnesium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.91841 Å / Relative weight: 1
Reflection
Resolution: 2.4→39.19 Å / Num. obs: 52805 / % possible obs: 99.8 % / Redundancy: 4.8 % / Biso Wilson estimate: 45.18 Å2
Reflection shell
Resolution: 2.4→2.53 Å / % possible all: 99.2
-
Processing
Software
Name
Version
Classification
MAR345
datacollection
BUSTER
2.10.0
refinement
XDS
datareduction
SCALA
datascaling
Refinement
Method to determine structure: Refined with PDB-ID 4A5B / Resolution: 2.4→24.19 Å / Cor.coef. Fo:Fc: 0.9434 / Cor.coef. Fo:Fc free: 0.9147 / SU R Cruickshank DPI: 0.349 / Cross valid method: THROUGHOUT / σ(F): 0 Details: THE ELECTRON DENSITY INDICATES BINDING OF THE ADENINE BASE OF AMPNP IN A PUTATIVE TGNTPDASE3 ADP-PRODUCT BINDING MODE. HOWEVER, DUE TO THE WEAK DENSITY THE OCCUPANCY OF THE LIGAND WAS SET TO 0.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.2131
1083
2.06 %
RANDOM
Rwork
0.1696
-
-
-
obs
0.1705
52612
99.65 %
-
Displacement parameters
Biso mean: 40.14 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-2.8767 Å2
0 Å2
0 Å2
2-
-
2.4129 Å2
0 Å2
3-
-
-
0.4637 Å2
Refine analyze
Luzzati coordinate error obs: 0.267 Å
Refinement step
Cycle: LAST / Resolution: 2.4→24.19 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
9277
0
38
504
9819
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
Restraint function
Weight
X-RAY DIFFRACTION
t_bond_d
0.01
9509
HARMONIC
2
X-RAY DIFFRACTION
t_angle_deg
1.16
12890
HARMONIC
2
X-RAY DIFFRACTION
t_dihedral_angle_d
3353
SINUSOIDAL
2
X-RAY DIFFRACTION
t_incorr_chiral_ct
X-RAY DIFFRACTION
t_pseud_angle
X-RAY DIFFRACTION
t_trig_c_planes
251
HARMONIC
2
X-RAY DIFFRACTION
t_gen_planes
1376
HARMONIC
5
X-RAY DIFFRACTION
t_it
9509
HARMONIC
20
X-RAY DIFFRACTION
t_nbd
0
SEMIHARMONIC
5
X-RAY DIFFRACTION
t_omega_torsion
3.02
X-RAY DIFFRACTION
t_other_torsion
17.61
X-RAY DIFFRACTION
t_improper_torsion
X-RAY DIFFRACTION
t_chiral_improper_torsion
1227
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
10809
SEMIHARMONIC
4
LS refinement shell
Resolution: 2.4→2.46 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.3184
77
2.06 %
Rwork
0.2047
3663
-
all
0.207
3740
-
obs
-
-
99.65 %
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
0.0154
0.6504
2.194
1.1754
-0.8687
0.6599
-0.0313
0.1974
-0.1356
0.1042
0.0011
0.0631
-0.0393
-0.0673
0.0302
-0.2861
0.0097
0.0315
0.2915
-0.0636
-0.0816
-6.8968
-27.8478
-92.8079
2
1.0295
0.1021
-0.4081
0.6194
-0.1811
2.1211
-0.0552
-0.0258
-0.1461
-0.0232
-0.0181
-0.022
0.2398
0.1079
0.0732
-0.1061
-0.0179
0.0158
-0.0815
0.0091
-0.0237
-12.4682
-27.8376
-45.2115
3
0.9096
-0.8529
1.4043
0.2822
0.4147
0.9062
0.0032
0.0275
0.0175
0.0668
-0.0061
0.0584
0.0036
0.015
0.0029
-0.051
-0.0026
0.0426
0.0586
0.0391
0.0189
-23.4005
0.2589
-61.6356
4
0.8621
0.2979
-0.1197
1.1059
-0.2842
0.659
0.0561
-0.0456
0.0318
0.0848
0.005
0.1614
-0.0559
-0.0933
-0.0611
-0.0887
0.0066
0.0269
-0.0459
0.0014
-0.0122
-36.4338
-19.904
-31.9183
5
0.066
-1.0023
2.0756
3.2046
0.125
1.6461
0.0171
-0.2024
0.0309
0.1799
-0.0766
0.1081
-0.1102
-0.041
0.0595
0.0307
-0.0337
0.0144
-0.0066
-0.0119
-0.0785
-19.3913
-18.13
-14.1925
6
0.7007
-2.6726
-1.3804
1.5424
0.2791
0
-0.0187
-0.0491
0.0131
0.002
0.0033
-0.0104
-0.0899
0.1481
0.0154
-0.0788
-0.1207
-0.0247
0.2936
0.0319
-0.1977
30.3116
14.1253
-73.9611
7
1.1729
-0.0355
-0.3985
0.7847
0.0192
1.2302
0.039
0.0837
0.0745
0.0158
-0.0234
-0.0075
-0.1436
0.0018
-0.0156
-0.0365
-0.0142
0.0096
-0.1074
-0.0062
-0.0448
-4.8795
14.2743
-41.4037
8
1.8018
-0.1919
0.3332
0
0.4071
0.5786
-0.0225
-0.0196
0.0193
-0.0284
-0.0129
-0.0123
0.0155
0.0379
0.0354
-0.0367
-0.0038
0.0123
0.0279
0.0517
0.0349
14.7488
-13.6779
-42.7071
9
0.6341
-0.3661
-0.2959
1.1376
0.2094
1.9116
0.0053
-0.2403
0.0854
0.268
0.0891
-0.1542
-0.3682
0.4833
-0.0943
-0.0161
-0.0988
-0.0058
-0.0564
-0.0289
-0.1426
-0.8558
6.7496
-14.4607
10
0.9563
-0.0767
-2.7132
0.5605
-2.0534
1.8375
-0.0065
-0.1264
-0.0276
0.1615
-0.0184
0.058
-0.0222
-0.1784
0.0249
0.0468
0.0091
0.1203
-0.0954
-0.0171
-0.0505
-25.4584
4.7077
-17.217
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Selection details
Auth asym-ID
Auth seq-ID
1
X-RAY DIFFRACTION
1
{A|34 - A|58}
A
34 - 58
2
X-RAY DIFFRACTION
2
{A|59 - A|256 A|586 - A|629}
A
59 - 256
3
X-RAY DIFFRACTION
2
{A|59 - A|256 A|586 - A|629}
A
586 - 629
4
X-RAY DIFFRACTION
3
{A|257 - A|268}
A
257 - 268
5
X-RAY DIFFRACTION
4
{A|269 - A|394 A|425 - A|585}
A
269 - 394
6
X-RAY DIFFRACTION
4
{A|269 - A|394 A|425 - A|585}
A
425 - 585
7
X-RAY DIFFRACTION
5
{A|395 - A|424}
A
395 - 424
8
X-RAY DIFFRACTION
6
{B|34 - B|58}
B
34 - 58
9
X-RAY DIFFRACTION
7
{B|59 - B|256 B|586 - B|629}
B
59 - 256
10
X-RAY DIFFRACTION
7
{B|59 - B|256 B|586 - B|629}
B
586 - 629
11
X-RAY DIFFRACTION
8
{B|257 - B|268}
B
257 - 268
12
X-RAY DIFFRACTION
9
{B|269 - B|394 B|425 - B|585}
B
269 - 394
13
X-RAY DIFFRACTION
9
{B|269 - B|394 B|425 - B|585}
B
425 - 585
14
X-RAY DIFFRACTION
10
{B|395 - B|424}
B
395 - 424
+
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