Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
-
Experimental details
-
Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
-
Sample preparation
Crystal
Density Matthews: 2.44 Å3/Da / Density % sol: 49.61 %
Crystal grow
Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8.8 Details: 100 mM Tris (pH 8.8), 50 mM MgCl2, 24% (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: 3→38.93 Å / Num. obs: 25182 / % possible obs: 93 % / Biso Wilson estimate: 51.87 Å2
-
Processing
Software
Name
Version
Classification
MAR345
datacollection
BUSTER
2.10.0
refinement
XDS
datareduction
SCALA
datascaling
Refinement
Method to determine structure: Refined with Refmac, PDB-ID 4A5B Resolution: 3→38.93 Å / Cor.coef. Fo:Fc: 0.8141 / Cor.coef. Fo:Fc free: 0.7239 / Cross valid method: THROUGHOUT / σ(F): 0 Details: AN ADDITIONAL ALTERNATIVE CONFORMATION OF THE ADENINE BASE OF AMPNP APPEARS POSSIBLE BASED ON THE 3.0 A ELECTRON DENSITY MAPS. THE DENSITY SUGGESTS THAT AMPNP WITH AN OCCUPANCY OF 0.8 ...Details: AN ADDITIONAL ALTERNATIVE CONFORMATION OF THE ADENINE BASE OF AMPNP APPEARS POSSIBLE BASED ON THE 3.0 A ELECTRON DENSITY MAPS. THE DENSITY SUGGESTS THAT AMPNP WITH AN OCCUPANCY OF 0.8 REPRESENTS THE PREDOMINANT BINDING MODE, BUT AN ADDITIONAL ALTERNATIVE BINDING MODE CANNOT BE EXCLUDED ON THE BASIS OF THE LIMITED RESOLUTION OF 3.0 A AND WAS SET TO AN OCCUPANCY OF 0.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.2431
524
2.08 %
RANDOM
Rwork
0.2078
-
-
-
obs
0.2085
25144
92.46 %
-
Displacement parameters
Biso mean: 36 Å2
Baniso -1
Baniso -2
Baniso -3
1-
11.3418 Å2
0 Å2
0 Å2
2-
-
11.9034 Å2
0 Å2
3-
-
-
-23.2451 Å2
Refine analyze
Luzzati coordinate error obs: 0.425 Å
Refinement step
Cycle: LAST / Resolution: 3→38.93 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
9229
0
38
0
9267
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
Restraint function
Weight
X-RAY DIFFRACTION
t_bond_d
0.007
9488
HARMONIC
2
X-RAY DIFFRACTION
t_angle_deg
0.97
12864
HARMONIC
2
X-RAY DIFFRACTION
t_dihedral_angle_d
3350
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
1367
HARMONIC
5
X-RAY DIFFRACTION
t_it
9488
HARMONIC
20
X-RAY DIFFRACTION
t_nbd
0
SEMIHARMONIC
5
X-RAY DIFFRACTION
t_omega_torsion
1.79
X-RAY DIFFRACTION
t_other_torsion
18.66
X-RAY DIFFRACTION
t_improper_torsion
X-RAY DIFFRACTION
t_chiral_improper_torsion
1225
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
10532
SEMIHARMONIC
4
LS refinement shell
Resolution: 3→3.12 Å / Total num. of bins used: 13
Rfactor
Num. reflection
% reflection
all
0.2518
2565
-
Rwork
-
2517
-
Rfree
-
-
1.87 %
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
0.6907
1.4632
-0.8716
0.0042
1.2387
0
0.0079
0.0222
-0.0562
-0.0174
-0.0223
0.0107
0.0264
0.002
0.0143
-0.0471
-0.0247
0.0336
0.1131
0.0064
-0.0442
-7.1238
-27.6342
-91.9848
2
1.5743
-0.069
-0.0352
0.8532
-0.2123
2.4004
-0.0087
-0.0021
-0.1454
-0.0275
-0.0293
-0.0852
0.1766
-0.0647
0.0381
-0.0329
-0.0376
0.0589
-0.0603
-0.008
-0.1248
-12.3848
-27.8827
-45.0513
3
0
0.0062
0.8697
0.1489
0.444
0.2657
0.0014
-0.0021
0.0105
-0.0186
0.0089
0.0253
-0.0545
-0.0224
-0.0103
0.0002
0.0599
-0.0029
0.0749
0.0545
-0.0407
-23.2076
0.1432
-61.5756
4
1.496
0.2885
0.1602
1.2424
0.0751
1.1503
-0.0185
-0.0335
0.0456
0.1622
0.118
0.2171
-0.0835
-0.1812
-0.0995
-0.0323
-0.01
0.0827
-0.0284
-0.0447
-0.1665
-35.8697
-19.7733
-31.8558
5
0
-0.7255
-0.8088
1.2584
-0.6856
1.1779
-0.0085
-0.0715
-0.0442
0.0424
-0.0375
0.0099
-0.0797
-0.0631
0.046
0.2036
-0.1344
0.0238
0.0047
-0.0417
-0.2077
-19.2083
-18.1333
-14.1284
6
0.169
-0.0527
0.7186
0.0002
0.8894
1.4471
-0.0064
-0.0218
0.0161
0.0475
-0.0266
-0.0354
-0.0009
0.0175
0.033
0.0471
-0.0964
-0.0036
0.0709
0.0343
-0.1139
28.8379
13.488
-73.074
7
2.5535
-0.422
-0.3034
1.0075
-0.071
1.2427
0.0252
-0.006
0.0821
-0.0857
-0.0293
-0.0021
-0.3088
0.0616
0.0041
0.0853
-0.0553
0.0521
-0.1171
-0.0305
-0.1695
-4.7846
14.145
-41.28
8
0.7562
0.6579
-1.6099
0.0808
0.1348
0
-0.0159
-0.0397
0.0249
0.0068
-0.0098
-0.0239
0.0387
-0.0011
0.0257
-0.0622
-0.0961
0.1324
0.0251
-0.0519
0.0201
14.8572
-13.7777
-42.6324
9
0.9411
-0.0828
0.1572
1.3152
-0.0131
2.1423
0.016
-0.2196
-0.0976
0.2693
0.0273
-0.2222
-0.2478
0.255
-0.0433
0.062
-0.0783
0.0288
-0.0197
-0.0034
-0.2805
-0.7162
6.8444
-14.3319
10
0
-0.9228
-1.8625
0.2286
-0.5412
1.1473
0
-0.0407
-0.0484
0.0411
-0.0297
-0.0074
-0.0505
-0.0383
0.0297
0.1632
-0.026
0.1213
-0.0217
-0.0042
-0.1395
-25.2325
4.5732
-17.1018
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Selection details
Auth asym-ID
Auth seq-ID
1
X-RAY DIFFRACTION
1
{A|35 - A|58}
A
35 - 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|37 - B|58}
B
37 - 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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