Mass: 18.015 Da / Num. of mol.: 102 / 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: 3.76 Å3/Da / Density % sol: 67.32 % Description: THE 3D STRUCTURE WAS SOLVED FROM A SAD DATASET MEASURED IN-HOUSE TO 2.4A AND A PRELIMINARY REFINEMENT CARRIED OUT. FOLLOWING A MOLECULAR REPLACEMENT STEP TO CORRECTLY POSITION THE ...Description: THE 3D STRUCTURE WAS SOLVED FROM A SAD DATASET MEASURED IN-HOUSE TO 2.4A AND A PRELIMINARY REFINEMENT CARRIED OUT. FOLLOWING A MOLECULAR REPLACEMENT STEP TO CORRECTLY POSITION THE RESULTING MODEL IN THE UNIT CELL OF THE CRYSTAL MEASURED AT THE ESRF, IT WAS USED IN THE FINAL REFINEMENT.
Crystal grow
pH: 8.5 Details: 85 MM TRISHCL PH 8.5, 8.5 MM NICL2, 15%(V/V) PEG 2000 MONOMETHYL ETHER AND 15%(V/V) GLYCEROL
Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.98 Å / Relative weight: 1
Reflection
Resolution: 1.85→47.2 Å / Num. obs: 18718 / % possible obs: 98.6 % / Observed criterion σ(I): 0 / Redundancy: 11.6 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 18.23
Reflection shell
Resolution: 1.85→1.96 Å / Redundancy: 11.6 % / Rmerge(I) obs: 0.92 / Mean I/σ(I) obs: 2.14 / % possible all: 98
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Processing
Software
Name
Version
Classification
PHENIX
(PHENIX.REFINE: 1.8.1_1168)
refinement
XDS
datareduction
XSCALE
datascaling
PHASER
phasing
Refinement
Method to determine structure: MOLECULAR REPLACEMENT Starting model: PRELIMINARY MODEL FROM SAD Resolution: 1.847→47.196 Å / SU ML: 0.14 / σ(F): 1.88 / Phase error: 22.61 / Stereochemistry target values: ML
Rfactor
Num. reflection
% reflection
Rfree
0.1995
968
5.2 %
Rwork
0.1777
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-
obs
0.1788
18715
98.68 %
Solvent computation
Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement step
Cycle: LAST / Resolution: 1.847→47.196 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
989
0
1
102
1092
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
X-RAY DIFFRACTION
f_bond_d
0.007
1023
X-RAY DIFFRACTION
f_angle_d
1.051
1394
X-RAY DIFFRACTION
f_dihedral_angle_d
14.831
382
X-RAY DIFFRACTION
f_chiral_restr
0.08
144
X-RAY DIFFRACTION
f_plane_restr
0.006
180
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
1.8469-1.9443
0.2956
145
0.2886
2444
X-RAY DIFFRACTION
98
1.9443-2.0661
0.2367
134
0.2306
2507
X-RAY DIFFRACTION
100
2.0661-2.2256
0.2442
128
0.206
2530
X-RAY DIFFRACTION
100
2.2256-2.4496
0.2343
152
0.1816
2515
X-RAY DIFFRACTION
99
2.4496-2.804
0.226
153
0.1832
2509
X-RAY DIFFRACTION
99
2.804-3.5326
0.1852
138
0.1674
2557
X-RAY DIFFRACTION
99
3.5326-47.2116
0.167
118
0.1596
2685
X-RAY DIFFRACTION
96
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
0.0036
0
-0.0209
0.009
0.0435
0.045
0.0505
-0.0708
0.508
-0.5365
0.0279
0.1647
0.0153
-0.2578
-0.0001
0.4613
-0.0455
0.0025
0.3027
-0.0156
0.3563
-50.2978
21.3123
3.8024
2
0.1927
0.0714
0.0763
0.0272
0.0256
0.1069
0.0135
0.5545
0.4151
-0.4601
0.2498
-0.3374
-1.3623
0.5706
0.0003
0.6126
-0.0939
0.0491
0.4068
0.0093
0.5333
-46.1868
22.2383
-8.1259
3
0.1349
-0.1057
-0.0276
0.0545
0.0449
-0.0024
-0.1726
0.3971
0.2316
-0.3702
0.2558
-0.3379
-0.5666
0.6003
-0.0004
0.4669
-0.0735
0.054
0.5031
0.0571
0.4831
-42.6526
15.401
-12.7641
4
0.256
-0.0815
0.0493
0.0637
0.2125
0.487
0.1463
0.8427
-0.1213
-0.3973
-0.1273
0.106
-0.2135
-0.0805
-0.0007
0.4584
0.0281
-0.0808
0.4792
0.0105
0.2761
-63.1849
8.4412
-20.556
5
0.0669
0.0464
0.0029
0.0283
0.0248
0.0432
0.3992
0.0452
-0.4091
-0.1296
0.3064
-0.3933
0.3725
0.3159
0.0007
0.3763
0.0039
0.0084
0.3689
-0.0669
0.5049
-38.4177
5.8239
-9.0085
6
0.1279
0.2175
-0.1758
0.3403
-0.0682
0.5177
0.0045
0.2906
0.2569
-0.0382
-0.0331
-0.0272
-0.1602
-0.1251
-0
0.3824
0.0474
-0.0306
0.2829
0.003
0.3632
-61.0067
12.5752
-5.812
7
0.2039
0.3155
0.1028
0.4676
0.2358
0.1998
-0.0417
-0.0746
0.0565
0.1607
-0.0848
-0.1293
-0.1354
0.1056
0
0.3467
0.0041
-0.0091
0.3073
0.022
0.3513
-49.8262
1.5538
-7.8358
8
0.0001
-0.0903
-0.0543
0.6542
0.0955
0.3841
-0.1021
0.0673
0.0039
-0.1255
0.082
-0.0299
-0.2273
0.057
0
0.3473
0.0276
-0.0178
0.307
0.0238
0.2959
-59.0455
9.3413
-11.9237
9
0.4129
-0.0031
-0.4459
0.4941
0.4565
0.6759
0.0059
-0.2822
0.4184
-0.1151
0.007
-0.0484
-0.2035
-0.2802
-0.0004
0.3974
0.0135
-0.019
0.2778
0.0594
0.4095
-54.1292
15.4585
-11.2044
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Selection details
1
X-RAY DIFFRACTION
1
CHAINAAND (RESID2THROUGH7 )
2
X-RAY DIFFRACTION
2
CHAINAAND (RESID8THROUGH16 )
3
X-RAY DIFFRACTION
3
CHAINAAND (RESID17THROUGH30 )
4
X-RAY DIFFRACTION
4
CHAINAAND (RESID31THROUGH46 )
5
X-RAY DIFFRACTION
5
CHAINAAND (RESID47THROUGH57 )
6
X-RAY DIFFRACTION
6
CHAINAAND (RESID58THROUGH74 )
7
X-RAY DIFFRACTION
7
CHAINAAND (RESID75THROUGH89 )
8
X-RAY DIFFRACTION
8
CHAINAAND (RESID90THROUGH109 )
9
X-RAY DIFFRACTION
9
CHAINAAND (RESID110THROUGH124 )
+
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