Mass: 18.015 Da / Num. of mol.: 72 / 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: 52.34 %
Crystal grow
Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.7 Details: 200 MM MES, 27% PEG8K, 200 MM AMMONIUM SULFATE, 1 MM MANGANESE CHLORIDE, 10 MM MAGNESIUM ACETATE, 10 MM TAURINE, AND 50 MM SODIUM FLUORIDE, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Monochromator: HORIZONTAL BENT SI(111), ASYMMETRICALLY CUT WITH WATER COOLED CU BLOCK Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 1.1 Å / Relative weight: 1
Reflection
Resolution: 2.2→50 Å / Num. obs: 15141 / % possible obs: 98.4 % / Observed criterion σ(I): -3 / Redundancy: 5.9 % / Rmerge(I) obs: 0.047 / Net I/σ(I): 36.72
Reflection shell
Resolution: 2.2→2.24 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.277 / Mean I/σ(I) obs: 3.4 / % possible all: 85
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Processing
Software
Name
Version
Classification
CBASS
datacollection
PHENIX
(PHENIX.REFINE: 1.8.2_1309)
modelbuilding
PHENIX
(phenix.refine: 1.8.2_1309)
refinement
HKL-2000
datareduction
HKL-2000
datascaling
PHENIX
1.8.2_1309
phasing
Refinement
Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→46.945 Å / SU ML: 0.25 / σ(F): 1.36 / Phase error: 22.19 / Stereochemistry target values: ML
Rfactor
Num. reflection
% reflection
Rfree
0.2063
726
5.03 %
Rwork
0.182
-
-
obs
0.1832
15141
96.95 %
Solvent computation
Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement step
Cycle: LAST / Resolution: 2.2→46.945 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
1646
0
34
72
1752
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
X-RAY DIFFRACTION
f_bond_d
0.006
1728
X-RAY DIFFRACTION
f_angle_d
1.016
2338
X-RAY DIFFRACTION
f_dihedral_angle_d
14.814
651
X-RAY DIFFRACTION
f_chiral_restr
0.038
241
X-RAY DIFFRACTION
f_plane_restr
0.004
296
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
2.1987-2.2773
0.27
115
0.2371
2154
X-RAY DIFFRACTION
78
2.2773-2.3685
0.2675
140
0.2376
2609
X-RAY DIFFRACTION
94
2.3685-2.4763
0.2656
147
0.2231
2710
X-RAY DIFFRACTION
98
2.4763-2.6068
0.2326
145
0.1969
2742
X-RAY DIFFRACTION
100
2.6068-2.7701
0.2283
148
0.1955
2773
X-RAY DIFFRACTION
100
2.7701-2.984
0.2237
135
0.1891
2745
X-RAY DIFFRACTION
100
2.984-3.2842
0.2748
148
0.1987
2743
X-RAY DIFFRACTION
100
3.2842-3.7592
0.1785
144
0.1853
2752
X-RAY DIFFRACTION
100
3.7592-4.7355
0.2044
141
0.1503
2768
X-RAY DIFFRACTION
100
4.7355-46.9561
0.167
153
0.1744
2745
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
6.4013
2.8921
-0.847
4.3885
-1.2857
4.9907
-0.358
0.2965
-0.4786
-0.2482
0.1226
-0.387
0.3312
0.3784
0.235
0.3521
-0.0905
-0.0089
0.298
0.0098
0.3678
19.0824
15.4642
-10.1732
2
5.0238
1.3816
0.6715
4.5282
-0.0159
6.0729
0.3134
-0.4155
-0.0183
0.4339
-0.4506
0.1583
0.1747
-0.4537
0.1079
0.2812
-0.1084
-0.0336
0.2944
0.0143
0.3623
6.772
14.0085
-2.4602
3
0.1487
-0.9539
0.5645
7.7696
-0.5622
7.9707
-0.1792
-0.6197
1.1281
-0.2873
-0.1015
1.585
-0.1005
-0.7451
0.2651
0.3917
-0.0875
-0.0975
0.2634
-0.0924
0.6842
4.4508
22.8516
0.1506
4
6.326
2.1444
-2.1132
2.2474
-0.2804
5.5851
0.0243
-0.2362
0.642
-0.1285
-0.1942
0.1592
-0.9236
0.5467
0.1013
0.5011
-0.1838
-0.0859
0.3633
-0.0418
0.4362
20.9764
25.7057
-2.128
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Selection details
Auth asym-ID
Auth seq-ID
1
X-RAY DIFFRACTION
1
( CHAIN A AND RESID -4:62 )
A
-4 - 62
2
X-RAY DIFFRACTION
2
( CHAINAANDRESID63:137 )
A
63 - 137
3
X-RAY DIFFRACTION
3
( CHAINAANDRESID138:149 )
A
138 - 149
4
X-RAY DIFFRACTION
4
( CHAINAANDRESID150:195 )
A
150 - 195
+
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