Mass: 18.015 Da / Num. of mol.: 160 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interest
Y
-
Experimental details
-
Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
-
Sample preparation
Crystal
Density Matthews: 2.08 Å3/Da / Density % sol: 40.96 % / Mosaicity: 0.26 °
Crystal grow
Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: Crystals grew in 0.1 M sodium acetate, 0.3 M sodium chloride at pH 4.6 in the presence of 0.1 M Lithium sulfate. After growth, and before measurement, these crystals were soaked in the dye ...Details: Crystals grew in 0.1 M sodium acetate, 0.3 M sodium chloride at pH 4.6 in the presence of 0.1 M Lithium sulfate. After growth, and before measurement, these crystals were soaked in the dye solution: saturated bromophenol blue, 0.3 M sodium chloride, 100 mM Lithium sulfate, 100 mM phosphate buffer at pH 7.0
-
Data collection
Diffraction
Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source
Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.979 Å
Resolution: 0.97→19.6 Å / SU ML: 0.0969 / Cross valid method: FREE R-VALUE / σ(F): 1.91 / Phase error: 19.7886 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 Details: The ligand geometry validation is not accurate because the molecule is a resonant form.
Rfactor
Num. reflection
% reflection
Rfree
0.1983
6932
5.06 %
Rwork
0.1731
130072
-
obs
0.1744
137004
98.87 %
Solvent computation
Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parameters
Biso mean: 14.21 Å2
Refinement step
Cycle: LAST / Resolution: 0.97→19.6 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
1001
0
59
160
1220
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
X-RAY DIFFRACTION
f_bond_d
0.0093
1110
X-RAY DIFFRACTION
f_angle_d
1.0561
1514
X-RAY DIFFRACTION
f_chiral_restr
0.0768
150
X-RAY DIFFRACTION
f_plane_restr
0.0055
193
X-RAY DIFFRACTION
f_dihedral_angle_d
21.733
423
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
0.97-0.98
0.3655
233
0.3033
4177
X-RAY DIFFRACTION
95.25
0.98-0.99
0.2977
238
0.2768
4284
X-RAY DIFFRACTION
98.52
0.99-1
0.2854
265
0.2605
4297
X-RAY DIFFRACTION
97.94
1-1.01
0.2881
198
0.2429
4319
X-RAY DIFFRACTION
97.98
1.01-1.03
0.2369
214
0.2376
4356
X-RAY DIFFRACTION
99.15
1.03-1.04
0.2446
249
0.2265
4382
X-RAY DIFFRACTION
98.91
1.04-1.06
0.2442
220
0.21
4293
X-RAY DIFFRACTION
99.51
1.06-1.07
0.2155
206
0.1961
4402
X-RAY DIFFRACTION
99.25
1.07-1.09
0.2295
219
0.1879
4380
X-RAY DIFFRACTION
99.2
1.09-1.11
0.215
245
0.1804
4334
X-RAY DIFFRACTION
99.09
1.11-1.13
0.1747
215
0.1739
4379
X-RAY DIFFRACTION
99.24
1.13-1.15
0.1996
233
0.1661
4307
X-RAY DIFFRACTION
99.1
1.15-1.17
0.1876
255
0.1666
4371
X-RAY DIFFRACTION
99.1
1.17-1.19
0.1493
238
0.1593
4310
X-RAY DIFFRACTION
99.43
1.19-1.22
0.1697
226
0.1641
4355
X-RAY DIFFRACTION
99.31
1.22-1.25
0.1776
219
0.1706
4359
X-RAY DIFFRACTION
99.54
1.25-1.28
0.2158
240
0.1701
4364
X-RAY DIFFRACTION
99.2
1.28-1.31
0.1909
226
0.1697
4401
X-RAY DIFFRACTION
99.42
1.31-1.35
0.1927
265
0.1765
4269
X-RAY DIFFRACTION
99.32
1.35-1.39
0.1929
247
0.1752
4356
X-RAY DIFFRACTION
99.52
1.39-1.44
0.2088
220
0.1661
4402
X-RAY DIFFRACTION
99.57
1.44-1.5
0.1824
203
0.1656
4378
X-RAY DIFFRACTION
99.46
1.5-1.57
0.1694
196
0.1662
4396
X-RAY DIFFRACTION
99.5
1.57-1.65
0.1853
222
0.1626
4345
X-RAY DIFFRACTION
99.24
1.65-1.76
0.1891
261
0.1681
4316
X-RAY DIFFRACTION
98.43
1.76-1.89
0.1751
193
0.1703
4349
X-RAY DIFFRACTION
98.52
1.89-2.08
0.1878
239
0.1645
4280
X-RAY DIFFRACTION
98.35
2.08-2.38
0.1975
257
0.1675
4306
X-RAY DIFFRACTION
98.49
2.38-3
0.1833
209
0.1673
4346
X-RAY DIFFRACTION
98.32
3-19.6
0.2134
281
0.1726
4259
X-RAY DIFFRACTION
98.57
+
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