Mass: 18.015 Da / Num. of mol.: 723 / 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: 2.17 Å3/Da / Density % sol: 43.22 %
Crystal grow
Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.3 Details: Protein: 11.2 mg/ml, 0.5 M sodium chloride, 0.01 M Tris-HCl, Screen: Pegs H1 (Qiagen), 0.2 M K/Na tartrate, 20% (w/v) PEG 3350 Crystals were soaked in a mother liquor containing 20 mM ...Details: Protein: 11.2 mg/ml, 0.5 M sodium chloride, 0.01 M Tris-HCl, Screen: Pegs H1 (Qiagen), 0.2 M K/Na tartrate, 20% (w/v) PEG 3350 Crystals were soaked in a mother liquor containing 20 mM arabinose-5-phosphate for 2 hours before being flash frozen for data collection, VAPOR DIFFUSION, SITTING DROP, temperature 295K, pH 8.3
Resolution: 1.5→30 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.965 / SU B: 1.939 / SU ML: 0.037 / Cross valid method: THROUGHOUT / ESU R Free: 0.064 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.17527
5316
5 %
RANDOM
Rwork
0.15056
-
-
-
all
0.15181
106919
-
-
obs
0.15181
101536
99.5 %
-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parameters
Biso mean: 18.775 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0.37 Å2
0 Å2
0 Å2
2-
-
0.28 Å2
0 Å2
3-
-
-
-0.65 Å2
Refinement step
Cycle: LAST / Resolution: 1.5→30 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
4847
0
79
723
5649
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.022
0.02
5210
X-RAY DIFFRACTION
r_bond_other_d
0.001
0.02
3556
X-RAY DIFFRACTION
r_angle_refined_deg
2.057
1.987
7073
X-RAY DIFFRACTION
r_angle_other_deg
1.04
3
8846
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
4.407
5
686
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
36.259
26.182
220
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
11.269
15
1020
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
14.272
15
19
X-RAY DIFFRACTION
r_chiral_restr
0.126
0.2
849
X-RAY DIFFRACTION
r_gen_planes_refined
0.01
0.02
5667
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
921
X-RAY DIFFRACTION
r_nbd_refined
X-RAY DIFFRACTION
r_nbd_other
X-RAY DIFFRACTION
r_nbtor_refined
X-RAY DIFFRACTION
r_nbtor_other
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
X-RAY DIFFRACTION
r_xyhbond_nbd_other
X-RAY DIFFRACTION
r_metal_ion_refined
X-RAY DIFFRACTION
r_metal_ion_other
X-RAY DIFFRACTION
r_symmetry_vdw_refined
X-RAY DIFFRACTION
r_symmetry_vdw_other
X-RAY DIFFRACTION
r_symmetry_hbond_refined
X-RAY DIFFRACTION
r_symmetry_hbond_other
X-RAY DIFFRACTION
r_symmetry_metal_ion_refined
X-RAY DIFFRACTION
r_symmetry_metal_ion_other
X-RAY DIFFRACTION
r_mcbond_it
X-RAY DIFFRACTION
r_mcbond_other
X-RAY DIFFRACTION
r_mcangle_it
X-RAY DIFFRACTION
r_scbond_it
X-RAY DIFFRACTION
r_scangle_it
X-RAY DIFFRACTION
r_rigid_bond_restr
X-RAY DIFFRACTION
r_sphericity_free
X-RAY DIFFRACTION
r_sphericity_bonded
LS refinement shell
Resolution: 1.502→1.541 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.232
345
-
Rwork
0.202
6707
-
obs
-
-
94.73 %
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
0.2079
-0.0124
0.2268
0.1182
-0.0105
0.3031
-0.083
0.0453
-0.0152
-0.0009
0.0229
0.0004
-0.1454
0.0283
0.0601
0.156
-0.0183
-0.0422
0.1046
-0.0049
0.125
-1.0374
22.5427
-14.5954
2
3.9907
0.1914
-1.6373
7.3547
3.6288
2.6386
0.4465
0.9252
0.3657
-0.4322
-0.4435
0.2934
-0.4445
-0.8233
-0.003
0.164
0.2087
-0.0308
0.6432
0.0587
0.0821
-22.7378
12.5689
-24.9235
3
0.1013
0.0775
-0.0017
0.2772
-0.1284
0.6087
-0.0506
0.0154
-0.0196
-0.0389
0.0066
-0.0278
0.0336
-0.0178
0.044
0.1173
-0.0093
0.0061
0.1008
-0.0029
0.0998
-5.5031
3.3552
-17.6389
4
0.2325
0.2256
0.2558
0.3754
0.1562
0.3442
0.0038
0.0046
0.0207
0.0611
-0.0501
0.0054
-0.0525
0.0518
0.0462
0.1249
-0.0317
-0.0053
0.1049
-0.0077
0.1093
2.9022
15.9749
-1.2081
5
0.0137
0.051
-0.0764
0.2348
-0.3456
0.5493
0.0021
-0.0168
-0.0118
0.0505
-0.0377
-0.0072
-0.0378
0.0065
0.0356
0.113
-0.013
-0.0066
0.1072
-0.0013
0.1127
-3.7589
4.0515
-1.1491
6
13.6274
-2.1856
6.0826
1.0142
1.7193
13.6673
0.5083
0.1828
-0.442
-0.1666
-0.2505
0.0632
-0.0972
-0.7397
-0.2578
0.0481
0.0805
-0.0555
0.2691
-0.0651
0.1249
-27.6381
9.8101
-17.6328
7
0.4615
0.0322
-0.4412
0.0077
-0.0513
0.8498
-0.0185
-0.1032
-0.0217
0.0148
-0.0137
-0.0013
0.1082
0.0465
0.0322
0.1172
-0.0271
0.0086
0.1406
0.004
0.0872
-19.8082
-19.8451
28.4047
8
2.7922
-0.996
-1.5191
0.4987
0.8582
1.6396
-0.0299
-0.2824
0.0216
0.0568
0.0871
-0.0764
0.1308
0.0461
-0.0572
0.072
0.0337
-0.0006
0.1629
-0.0139
0.1506
5.1794
-24.0805
25.8945
9
0.188
-0.0313
-0.1537
0.1474
-0.1141
0.3285
-0.0162
-0.0184
-0.0295
-0.0289
-0.0056
-0.008
0.0211
0.0088
0.0218
0.1051
-0.007
0.0069
0.1082
0.0013
0.1069
-11.7574
-20.0804
13.1096
10
0.0667
0.0846
-0.0771
0.1408
-0.0631
0.4182
0.0216
-0.0153
0.0104
0.0256
-0.0084
0.0637
-0.0263
-0.047
-0.0131
0.1006
-0.0065
0.0095
0.1338
-0.014
0.1048
-26.6891
-10.7752
18.786
11
0.7556
-0.321
-0.116
2.3347
-0.7893
0.3586
-0.0335
0.0483
0.0355
0.1095
0.1783
0.3141
-0.0654
-0.152
-0.1448
0.0737
0.0692
0.0467
0.3172
0.007
0.0837
-36.6194
-12.5275
25.7792
12
0.1112
0.0367
-0.0816
0.2021
-0.2495
0.3908
0.0186
-0.0459
0.0188
-0.0199
0.005
-0.039
-0.041
0.009
-0.0235
0.1066
-0.011
0.0085
0.1153
-0.0122
0.1212
-7.2372
-9.0849
10.7373
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Auth asym-ID
Auth seq-ID
1
X-RAY DIFFRACTION
1
A
1 - 44
2
X-RAY DIFFRACTION
2
A
45 - 70
3
X-RAY DIFFRACTION
3
A
71 - 176
4
X-RAY DIFFRACTION
4
A
177 - 261
5
X-RAY DIFFRACTION
5
A
262 - 313
6
X-RAY DIFFRACTION
6
A
314 - 321
7
X-RAY DIFFRACTION
7
B
3 - 44
8
X-RAY DIFFRACTION
8
B
45 - 76
9
X-RAY DIFFRACTION
9
B
77 - 194
10
X-RAY DIFFRACTION
10
B
195 - 258
11
X-RAY DIFFRACTION
11
B
259 - 268
12
X-RAY DIFFRACTION
12
B
279 - 321
+
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