Mass: 18.015 Da / Num. of mol.: 154 / Source method: isolated from a natural source / Formula: H2O
-
Experimental details
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Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
-
Sample preparation
Crystal
Density Matthews: 2.42 Å3/Da / Density % sol: 49.26 %
Crystal grow
Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: WELL SOLUTION: 25% PEG 3350, 0.1 M NH4 SULPHATE, 0.1 M HEPES PH 7.5. PROTEIN SOLUTION: 15 MG/ML. DROPS: 1:1 RATIO OF WELL:PROTEIN SOLUTION. CRYSTALS CRYOPROTECTED BY TRANSFER TO DROP ...Details: WELL SOLUTION: 25% PEG 3350, 0.1 M NH4 SULPHATE, 0.1 M HEPES PH 7.5. PROTEIN SOLUTION: 15 MG/ML. DROPS: 1:1 RATIO OF WELL:PROTEIN SOLUTION. CRYSTALS CRYOPROTECTED BY TRANSFER TO DROP CONTAINING MOTHER LIQUOR TO WHICH MPD WAS ADDED TO 25%, , pH 7.50, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K
Resolution: 2→23.69 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.931 / SU B: 8.289 / SU ML: 0.119 / Cross valid method: THROUGHOUT / ESU R: 0.179 / ESU R Free: 0.161 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS, ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.2316
1062
4.9 %
RANDOM
Rwork
0.18917
-
-
-
obs
0.19118
20747
95.3 %
-
all
-
21809
-
-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parameters
Biso mean: 27.811 Å2
Baniso -1
Baniso -2
Baniso -3
1-
1.06 Å2
0.53 Å2
0 Å2
2-
-
1.06 Å2
0 Å2
3-
-
-
-1.59 Å2
Refinement step
Cycle: LAST / Resolution: 2→23.69 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
2172
0
30
156
2358
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.011
0.022
2254
X-RAY DIFFRACTION
r_angle_refined_deg
1.156
1.963
3057
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.13
5
278
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
32.222
23.529
102
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
12.401
15
372
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
20.531
15
17
X-RAY DIFFRACTION
r_chiral_restr
0.079
0.2
328
X-RAY DIFFRACTION
r_gen_planes_refined
0.004
0.02
1733
X-RAY DIFFRACTION
r_nbd_refined
0.195
0.2
1067
X-RAY DIFFRACTION
r_nbtor_refined
0.3
0.2
1562
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.121
0.2
144
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.155
0.2
41
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.107
0.2
14
X-RAY DIFFRACTION
r_mcbond_it
0.599
1.5
1433
X-RAY DIFFRACTION
r_mcangle_it
0.939
2
2223
X-RAY DIFFRACTION
r_scbond_it
1.451
3
961
X-RAY DIFFRACTION
r_scangle_it
2.329
4.5
834
LS refinement shell
Resolution: 2→2.052 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.242
93
-
Rwork
0.212
1549
-
obs
-
-
97.8 %
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
52.3212
-10.2619
3.0468
16.7594
-4.1977
1.2027
-1.3328
-3.8486
-0.8284
1.6378
1.4336
2.3378
-0.8689
-0.259
-0.1008
0.5822
0.2976
0.2799
0.398
-0.0178
0.3728
-23.5049
15.895
6.7817
2
5.6051
-4.3126
6.4159
15.8154
-12.0783
29.9614
-0.0209
-0.1316
0.1512
1.0372
0.2688
-0.1928
-0.1092
0.3311
-0.2479
0.2177
0.0751
0.0634
-0.0546
-0.0442
0.1554
-24.5506
23.3388
-2.2199
3
3.5596
-1.44
-1.7272
15.3352
3.3101
11.4513
-0.0798
0.2148
-0.2242
0.3223
-0.0615
0.4156
0.8852
-0.1297
0.1413
0.2131
0.0652
-0.0064
0.0183
0.0334
0.1242
-26.3481
16.8901
-19.0731
4
6.3916
-2.6059
0.8989
1.082
-0.0721
4.5529
-0.1467
-0.2665
-0.1607
0.1439
-0.0111
-0.0156
0.3753
-0.3753
0.1579
0.358
0.0244
0.0712
0.0023
-0.0142
0.1223
-24.1384
15.7756
-8.054
5
0.9278
-1.0216
0.0987
1.7382
0.0568
0.0551
0.1714
0.1004
0.0465
-0.1808
-0.0892
-0.0147
-0.1583
-0.0306
-0.0822
0.2173
0.0149
0.031
0.1042
0.0066
0.1338
-12.5487
7.8593
-11.7383
6
0.9816
0.3196
-0.6064
2.3233
0.268
2.4454
0.066
0.0866
-0.0768
0.0556
-0.0729
0.0815
0.1043
-0.2141
0.0069
0.1343
0.0006
0.0059
0.1158
-0.0028
0.1558
-11.9762
-5.2213
-4.536
7
1.3403
0.0946
-0.1955
3.8604
0.6872
3.6522
-0.0602
-0.0963
-0.114
0.2218
0.0203
-0.259
0.2027
0.2173
0.04
0.1136
0.0216
-0.0191
0.0881
-0.0076
0.1843
-2.4782
-7.6459
-2.1622
8
15.6746
-2.6792
16.0375
96.0936
-32.015
25.3694
-2.0645
-2.919
-1.9897
2.7216
4.9309
-4.0892
-1.1194
-0.8358
-2.8664
0.5296
0.0908
0.15
0.6858
-0.1846
0.4681
11.407
-0.3139
-12.0321
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Auth asym-ID
Label asym-ID
Auth seq-ID
Label seq-ID
1
X-RAY DIFFRACTION
1
A
A
607 - 618
19 - 30
2
X-RAY DIFFRACTION
2
A
A
619 - 628
31 - 40
3
X-RAY DIFFRACTION
3
A
A
629 - 654
41 - 66
4
X-RAY DIFFRACTION
4
A
A
655 - 696
67 - 108
5
X-RAY DIFFRACTION
5
A
A
697 - 770
109 - 182
6
X-RAY DIFFRACTION
6
A
A
771 - 841
183 - 253
7
X-RAY DIFFRACTION
7
A
A
842 - 893
254 - 305
8
X-RAY DIFFRACTION
8
A
A
894 - 902
306 - 314
+
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