Mass: 18.015 Da / Num. of mol.: 36 / 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: 2.5 Å3/Da / Density % sol: 50 % Description: THE SEARCH MODEL USED WAS A PRELIMINARY AND REFINED SAD DATASET MEASURED IN-HOUSE TO 2.0A.
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.98008 Å / Relative weight: 1
Reflection
Resolution: 2→31.92 Å / Num. obs: 8422 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Biso Wilson estimate: 31.44 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 13
Reflection shell
Resolution: 2→2.1 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.78 / Mean I/σ(I) obs: 2.2 / % possible all: 100
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Processing
Software
Name
Version
Classification
PHENIX
(PHENIX.REFINE)
refinement
XDS
datareduction
SCALA
datascaling
PHASER
phasing
Refinement
Method to determine structure: MOLECULAR REPLACEMENT Starting model: PRELIMINARY MODEL FROM SAD Resolution: 2.001→31.915 Å / SU ML: 0.23 / σ(F): 1.36 / Phase error: 26.6 / Stereochemistry target values: ML
Rfactor
Num. reflection
% reflection
Rfree
0.231
405
4.8 %
Rwork
0.1946
-
-
obs
0.1963
8417
99.81 %
Solvent computation
Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parameters
Biso mean: 38 Å2
Refinement step
Cycle: LAST / Resolution: 2.001→31.915 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
755
0
1
36
792
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
X-RAY DIFFRACTION
f_bond_d
0.012
778
X-RAY DIFFRACTION
f_angle_d
1.12
1055
X-RAY DIFFRACTION
f_dihedral_angle_d
15.973
284
X-RAY DIFFRACTION
f_chiral_restr
0.044
113
X-RAY DIFFRACTION
f_plane_restr
0.006
133
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
2.0006-2.29
0.3184
139
0.2327
2634
X-RAY DIFFRACTION
100
2.29-2.8849
0.2575
143
0.2267
2640
X-RAY DIFFRACTION
100
2.8849-31.9193
0.1988
123
0.1752
2738
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
1.3425
0.0819
-0.4463
0.1411
-0.2742
0.6264
0.0288
0.0572
0.3254
0.2331
0.0806
-0.2369
0.0652
-0.0935
0.32
0.4369
-0.0424
-0.2516
0.2165
-0.1485
0.4966
5.7303
106.6105
57.3725
2
0.1475
0.0701
0.0111
0.382
-0.4554
0.6765
-0.0518
-0.2257
0.3874
0.7432
-0.0648
-0.649
-0.234
0.093
0.1572
0.233
-0.0528
-0.1389
0.2027
-0.0144
0.5264
5.6449
101.3946
52.2741
3
0.0591
-0.0422
-0.0464
0.1235
0.0707
0.0512
-0.0187
-0.0854
0.0383
0.0312
-0.0712
0.0918
0.0311
-0.1182
-0.0666
0.6126
-0.0213
0.3926
0.377
-0.09
0.5856
-17.0893
97.1596
61.6666
4
0.4882
-0.0377
0.1532
0.0224
-0.0253
0.0709
-0.1627
0.1499
0.1285
0.3664
-0.1498
-0.0776
-0.0153
0.0801
-0.0504
0.1886
-0.0056
-0.01
0.1587
0.0155
0.2967
1.6852
98.4714
47.768
5
0.0043
-0.0007
0.0324
-0.0014
0.0023
0.276
-0.0678
-0.1042
0.0039
0.2228
0.0715
0.2058
-0.1074
-0.1051
0.0881
0.2198
0.0684
0.1012
0.3429
-0.2896
0.5813
-15.498
103.5709
54.563
6
0.3172
0.1631
-0.1869
0.2647
-0.0848
0.2198
0.1537
-0.3261
-0.0978
0.7226
-0.2152
-0.1691
-0.0806
0.0363
-0.0115
0.4696
-0.0428
-0.0844
0.2283
-0.0387
0.3349
2.0579
99.2784
59.5821
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Selection details
1
X-RAY DIFFRACTION
1
CHAIN 'A' AND (RESID16THROUGH26 )
2
X-RAY DIFFRACTION
2
CHAIN 'A' AND (RESID27THROUGH56 )
3
X-RAY DIFFRACTION
3
CHAIN 'A' AND (RESID57THROUGH62 )
4
X-RAY DIFFRACTION
4
CHAIN 'A' AND (RESID63THROUGH83 )
5
X-RAY DIFFRACTION
5
CHAIN 'A' AND (RESID84THROUGH91 )
6
X-RAY DIFFRACTION
6
CHAIN 'A' AND (RESID92THROUGH111 )
+
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