Mass: 18.015 Da / Num. of mol.: 192 / Source method: isolated from a natural source / Formula: H2O
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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: 2.58 Å3/Da / Density % sol: 52.4 % / Description: NONE
Crystal grow
pH: 4.2 Details: 0.2 M NACL; 0.1 M PHOSPHATE-CITRATE PH 4.2; 10%(W/V) GLYCEROL; 0.5 MM L-LYSINE AMIDE; PRIOR TO CRYO-COOLING, 30% (V/V) WERE ADDED AS A CRYOPROTECTANT
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Data collection
Diffraction
Mean temperature: 100 K
Diffraction source
Source: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.033184
Detector
Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 25, 2013 / Details: SI-111 AND SI-113 REFLECTION
Radiation
Monochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 1.033184 Å / Relative weight: 1
Reflection
Resolution: 2.1→37.34 Å / Num. obs: 36408 / % possible obs: 80.6 % / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Biso Wilson estimate: 27.47 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 8.7
Reflection shell
Resolution: 2.1→2.18 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 2.1 / % possible all: 19
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Processing
Software
Name
Version
Classification
PHENIX
(PHENIX.REFINE)
refinement
XDS
datareduction
XDS
datascaling
PHASER
phasing
Refinement
Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→37.337 Å / SU ML: 0.31 / σ(F): 1.97 / Phase error: 29.13 / Stereochemistry target values: ML
Rfactor
Num. reflection
% reflection
Rfree
0.2477
1820
5 %
Rwork
0.1972
-
-
obs
0.1998
36401
80.57 %
Solvent computation
Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parameters
Biso mean: 36 Å2
Refinement step
Cycle: LAST / Resolution: 2.1→37.337 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
5170
0
26
192
5388
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
X-RAY DIFFRACTION
f_bond_d
0.002
5378
X-RAY DIFFRACTION
f_angle_d
0.541
7230
X-RAY DIFFRACTION
f_dihedral_angle_d
10.628
2010
X-RAY DIFFRACTION
f_chiral_restr
0.02
733
X-RAY DIFFRACTION
f_plane_restr
0.003
937
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
2.1001-2.1569
0.3452
28
0.2873
592
X-RAY DIFFRACTION
18
2.1569-2.2203
0.3628
51
0.2636
949
X-RAY DIFFRACTION
29
2.2203-2.292
0.3467
89
0.2665
1450
X-RAY DIFFRACTION
45
2.292-2.3739
0.3154
123
0.2644
2522
X-RAY DIFFRACTION
76
2.3739-2.4689
0.309
162
0.2599
3208
X-RAY DIFFRACTION
96
2.4689-2.5812
0.3091
171
0.2563
3184
X-RAY DIFFRACTION
97
2.5812-2.7173
0.296
156
0.2481
3229
X-RAY DIFFRACTION
98
2.7173-2.8875
0.2694
184
0.2346
3230
X-RAY DIFFRACTION
98
2.8875-3.1103
0.2969
188
0.2213
3216
X-RAY DIFFRACTION
98
3.1103-3.4231
0.265
169
0.197
3231
X-RAY DIFFRACTION
98
3.4231-3.918
0.2053
175
0.1709
3275
X-RAY DIFFRACTION
98
3.918-4.9345
0.2008
159
0.1397
3217
X-RAY DIFFRACTION
98
4.9345-37.3424
0.18
165
0.1641
3278
X-RAY DIFFRACTION
99
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
1.4546
-0.8226
-0.016
0.5151
0.0856
0.3962
0.0463
0.4087
-0.5822
-0.2736
-0.0636
0.2536
0.0383
-0.2013
0.0115
0.2482
0.0031
-0.0466
0.2655
-0.0916
0.1652
27.8398
56.2777
7.922
2
0.3319
0.2143
0.0344
0.3202
0.1759
0.3154
0.0434
-0.2803
-0.0964
0.0608
-0.0773
0.0465
0.096
0.0364
-0.0131
0.1163
-0.022
-0.0093
0.1354
0.0278
0.0937
22.1146
57.3673
34.5258
3
0.986
-0.1869
-0.3798
0.2189
-0.032
0.2001
-0.022
-0.1319
-0.3471
0.0701
-0.1003
0.0127
0.0865
0.0453
-0.168
0.2084
-0.0308
0.0073
0.1372
0.0165
0.0633
20.8796
53.5928
34.8774
4
0.03
-0.0288
-0.0754
0.0498
0.1132
0.2149
-0.2627
0.0737
-0.1362
0.0025
0.1615
-0.0629
0.1658
0.0484
-0.028
0.1508
0.0069
-0.0405
0.2488
0.0154
0.3115
39.8056
55.3811
28.8775
5
0.067
0.0329
-0.0095
0.0506
0.0141
0.0257
0.0193
-0.0005
-0.1084
0.0212
-0.0888
-0.1517
0.1258
0.1455
-0.0007
0.1554
0.015
0.0197
0.1608
-0.0021
0.1839
39.4389
62.1711
16.8329
6
0.2144
0.0536
0.1137
0.1637
-0.1252
0.2481
0.2495
-0.1615
0.076
0.2849
-0.1434
0.0712
-0.0795
0.0008
0.0543
0.1895
-0.0346
0.0262
0.1926
-0.0605
0.1849
8.3336
19.8668
33.0342
7
0.6691
0.0797
0.0061
0.9515
-0.1872
0.3904
0.0433
0.13
0.1851
-0.036
-0.0937
0.0666
-0.0717
0.0451
-0.1515
0.0785
0.0131
0.0034
0.0982
0.0049
0.1002
17.5007
20.5353
14.0447
8
0.0935
0.0138
0.0769
0.213
-0.0248
0.0497
0.1139
0.1246
0.0326
-0.1231
-0.076
-0.0039
0.0787
0.0974
0.0001
0.1236
0.0172
0.0018
0.1661
0.0388
0.1132
21.2095
15.8869
8.1777
9
0.0542
0.0202
0.023
0.0107
0.0117
-0.0005
0.0068
0.0151
0.169
-0.2689
-0.0479
0.1381
-0.1314
-0.0995
0.0472
0.2117
0.0286
-0.0556
0.1753
0.0705
0.229
10.4281
26.742
7.3617
10
0.1618
0.181
-0.1157
0.2002
-0.1245
0.0928
0.1291
-0.0435
0.4162
0.1318
-0.0359
0.2804
-0.3595
-0.0124
0.2426
0.2357
0.0353
0.109
-0.0205
-0.1103
0.523
6.2056
34.3695
22.4188
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Selection details
1
X-RAY DIFFRACTION
1
CHAIN 'A' AND (RESID523THROUGH625 )
2
X-RAY DIFFRACTION
2
CHAIN 'A' AND (RESID626THROUGH715 )
3
X-RAY DIFFRACTION
3
CHAIN 'A' AND (RESID716THROUGH766 )
4
X-RAY DIFFRACTION
4
CHAIN 'A' AND (RESID767THROUGH819 )
5
X-RAY DIFFRACTION
5
CHAIN 'A' AND (RESID820THROUGH850 )
6
X-RAY DIFFRACTION
6
CHAIN 'B' AND (RESID523THROUGH602 )
7
X-RAY DIFFRACTION
7
CHAIN 'B' AND (RESID603THROUGH715 )
8
X-RAY DIFFRACTION
8
CHAIN 'B' AND (RESID716THROUGH765 )
9
X-RAY DIFFRACTION
9
CHAIN 'B' AND (RESID766THROUGH819 )
10
X-RAY DIFFRACTION
10
CHAIN 'B' AND (RESID820THROUGH848 )
+
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