Mass: 18.015 Da / Num. of mol.: 154 / 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
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Sample preparation
Crystal
Density Matthews: 2.24 Å3/Da / Density % sol: 45.12 %
Crystal grow
Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 18% PEG 3350, 0.2 M AmFormate
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Data collection
Diffraction
ID
Mean temperature (K)
Crystal-ID
1
100
1
2
100
1
Diffraction source
Source
Site
Beamline
ID
Wavelength (Å)
SYNCHROTRON
APS
22-BM
1
1
SYNCHROTRON
APS
22-ID
2
0.9792
Detector
Type
ID
Detector
Date
MARMOSAIC 225 mm CCD
1
CCD
Jul 28, 2011
MARMOSAIC 300 mm CCD
2
CCD
Aug 17, 2011
Radiation
ID
Protocol
Monochromatic (M) / Laue (L)
Scattering type
Wavelength-ID
1
SINGLEWAVELENGTH
M
x-ray
1
2
SINGLEWAVELENGTH
M
x-ray
2
Radiation wavelength
ID
Wavelength (Å)
Relative weight
1
1
1
2
0.9792
1
Reflection
Resolution: 2.35→20 Å / Num. obs: 26635 / % possible obs: 98.5 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.099 / Net I/σ(I): 11.8
Reflection shell
Resolution: 2.35→2.43 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.354 / Mean I/σ(I) obs: 2.6 / % possible all: 88.2
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Processing
Software
Name
Version
Classification
PHENIX
1.9_1692
refinement
HKL-2000
datareduction
HKL-2000
datascaling
PHENIX
phasing
Refinement
Method to determine structure: SAD / Resolution: 2.3551→19.968 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.07 / Stereochemistry target values: ML
Rfactor
Num. reflection
% reflection
Rfree
0.2391
1330
5 %
Rwork
0.1904
-
-
obs
0.1929
26626
98.02 %
Solvent computation
Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement step
Cycle: LAST / Resolution: 2.3551→19.968 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
4864
0
3
154
5021
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
X-RAY DIFFRACTION
f_bond_d
0.003
5030
X-RAY DIFFRACTION
f_angle_d
0.531
6767
X-RAY DIFFRACTION
f_dihedral_angle_d
13.325
1910
X-RAY DIFFRACTION
f_chiral_restr
0.02
715
X-RAY DIFFRACTION
f_plane_restr
0.002
881
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
2.3551-2.4492
0.2568
120
0.2251
2424
X-RAY DIFFRACTION
85
2.4492-2.5605
0.2916
142
0.2312
2786
X-RAY DIFFRACTION
98
2.5605-2.6952
0.2746
148
0.2228
2781
X-RAY DIFFRACTION
100
2.6952-2.8636
0.2862
133
0.2218
2872
X-RAY DIFFRACTION
100
2.8636-3.0839
0.2692
163
0.2248
2858
X-RAY DIFFRACTION
100
3.0839-3.3929
0.2539
154
0.2063
2834
X-RAY DIFFRACTION
100
3.3929-3.8807
0.2449
146
0.1804
2846
X-RAY DIFFRACTION
100
3.8807-4.8775
0.1968
148
0.157
2924
X-RAY DIFFRACTION
100
4.8775-19.9689
0.2033
176
0.1597
2971
X-RAY DIFFRACTION
100
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
2.3007
0.7163
1.7091
0.5434
0.7533
2.3803
0.0211
-0.1765
-0.1717
0.051
0.0264
-0.0683
0.0598
0.2349
-0.0517
0.2589
0.0099
0.0398
0.2597
0.031
0.216
56.6314
7.5824
22.8972
2
2.5253
0.0237
2.8657
1.2184
0.3401
6.659
-0.0295
0.1407
-0.1124
0.0775
-0.0197
0.2956
0.43
0.098
-0.075
0.3319
-0.0205
-0.0424
0.4466
0.0197
0.3268
89.2842
14.2926
61.7235
3
2.1579
0.4497
1.3565
0.4456
-0.4958
3.9313
-0.2236
0.4129
-0.0395
0.1823
-0.2047
-0.1266
-0.5808
0.9937
0.0341
0.3498
-0.0184
-0.0035
0.4329
0.0243
0.3261
97.5122
17.7846
73.2149
4
2.1837
0.4445
1.7311
0.3499
0.5404
2.5395
-0.236
0.2011
0.0998
-0.0907
0.0365
0.0765
-0.2012
0.2621
0.1181
0.1922
-0.0056
0.043
0.1442
0.0034
0.2203
41.5164
9.829
4.9098
5
0.7328
-0.7119
-0.4359
1.6718
-1.0048
2.3506
-0.0268
0.1602
-0.2821
0.0209
-0.2035
-0.4453
0.5458
-0.1287
-0.3232
1.2029
0.0184
0.0079
1.3529
-0.518
1.0386
-0.2921
-22.0235
-40.4451
6
2.3687
0.4362
1.9761
1.615
1.3556
5.7206
-0.4501
0.5425
0.0213
-0.6757
0.3344
0.1119
-0.6011
-0.2544
0.0447
0.3139
0.0158
-0.006
0.5117
-0.0703
0.4756
9.1471
-1.1496
-26.6539
7
2.185
0.7264
1.4677
0.7454
0.9771
2.5007
0.1722
-0.3653
-0.1758
0.155
-0.1842
0.1349
0.4656
-0.3783
0.0381
0.2789
-0.0327
0.0733
0.167
0.0274
0.2776
29.1816
1.3374
9.4744
8
1.2639
1.7996
0.6969
2.0048
0.8836
0.6973
0.2241
0.1848
-0.7414
-0.1392
0.0918
-0.7242
0.1765
0.0184
-0.1061
0.6796
-0.1569
-0.1059
0.6885
-0.2308
0.9429
-7.0529
-32.6901
-35.1097
9
3.0129
1.666
1.699
2.017
1.64
2.5431
0.05
0.0607
0.1297
0.0159
-0.2672
0.4813
0.2236
-0.6492
0.2081
0.3054
-0.076
0.0108
0.4003
-0.1195
0.495
2.0364
-9.097
-20.3554
10
2.574
0.4981
2.2541
0.5527
0.3748
1.7725
-0.2511
-0.5075
0.3277
0.0945
-0.0675
0.0587
-0.2173
-0.1275
0.1316
0.2549
0.0212
0.0219
0.4036
-0.057
0.2219
53.9561
20.2569
30.2243
11
1.2525
-0.3881
-1.1848
2.3339
0.1358
1.134
0.2581
-0.4955
0.1713
0.297
0.6076
-0.0054
0.3457
-0.377
-0.1311
1.1472
0.0471
0.0185
1.5021
-0.1764
0.7745
89.1443
26.4056
73.0567
12
3.3649
1.1027
1.9686
2.5045
2.1879
4.5266
-0.7059
-0.7182
0.4693
0.4836
0.052
-0.2068
-0.3644
0.3426
0.0722
0.9033
0.0688
-0.1861
0.7155
-0.0596
0.4953
78.3237
31.3226
49.6721
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Selection details
1
X-RAY DIFFRACTION
1
(chainAandresid5:119)
2
X-RAY DIFFRACTION
2
(chainAandresid120:150)
3
X-RAY DIFFRACTION
3
(chainAandresid151:206)
4
X-RAY DIFFRACTION
4
(chainAandresid207:281)
5
X-RAY DIFFRACTION
5
(chainAandresid282:292)
6
X-RAY DIFFRACTION
6
(chainAandresid293:302)
7
X-RAY DIFFRACTION
7
(chainBandresid5:123)
8
X-RAY DIFFRACTION
8
(chainBandresid124:176)
9
X-RAY DIFFRACTION
9
(chainBandresid177:221)
10
X-RAY DIFFRACTION
10
(chainBandresid222:283)
11
X-RAY DIFFRACTION
11
(chainBandresid284:292)
12
X-RAY DIFFRACTION
12
(chainBandresid293:302)
+
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