Mass: 18.015 Da / Num. of mol.: 207 / Source method: isolated from a natural source / Formula: H2O
-
Details
Has ligand of interest
Y
-
Experimental details
-
Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
-
Sample preparation
Crystal
Density Matthews: 2.12 Å3/Da / Density % sol: 41.92 % / Mosaicity: 0.53 °
Crystal grow
Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.3 M sodium chloride, 0.1 M imidazole. After growth, and before measurement, these crystals were soaked in the dye solution: saturated bromophenol blue, 0.3 M sodium chloride, 0.1 M imidazole buffer at pH 6.5.
-
Data collection
Diffraction
Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source
Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97926 Å
Resolution: 1.38→19.39 Å / SU ML: 0.1376 / Cross valid method: FREE R-VALUE / σ(F): 1.91 / Phase error: 21.5892 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
0.2261
4572
5.07 %
Rwork
0.191
85624
-
obs
0.1928
90196
94.01 %
Solvent computation
Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parameters
Biso mean: 17.47 Å2
Refinement step
Cycle: LAST / Resolution: 1.38→19.39 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
1992
0
240
207
2439
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
X-RAY DIFFRACTION
f_bond_d
0.0072
2294
X-RAY DIFFRACTION
f_angle_d
0.8965
3142
X-RAY DIFFRACTION
f_chiral_restr
0.0666
295
X-RAY DIFFRACTION
f_plane_restr
0.0045
387
X-RAY DIFFRACTION
f_dihedral_angle_d
25.037
453
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
1.38-1.4
0.3017
130
0.2429
2817
X-RAY DIFFRACTION
90.57
1.4-1.42
0.2558
147
0.2241
2670
X-RAY DIFFRACTION
89.03
1.42-1.43
0.2572
149
0.214
2719
X-RAY DIFFRACTION
89.4
1.43-1.45
0.2589
180
0.2222
2899
X-RAY DIFFRACTION
94.71
1.45-1.47
0.2569
156
0.203
2899
X-RAY DIFFRACTION
97.29
1.47-1.49
0.2342
143
0.2003
2919
X-RAY DIFFRACTION
96.17
1.49-1.51
0.2654
133
0.1923
3001
X-RAY DIFFRACTION
96.4
1.51-1.53
0.2321
162
0.199
2888
X-RAY DIFFRACTION
95.58
1.53-1.56
0.2497
138
0.1947
2994
X-RAY DIFFRACTION
97.45
1.56-1.58
0.2301
143
0.1894
2924
X-RAY DIFFRACTION
97.09
1.58-1.61
0.2424
179
0.1886
2907
X-RAY DIFFRACTION
96.95
1.61-1.64
0.2142
157
0.1832
2986
X-RAY DIFFRACTION
96.71
1.64-1.67
0.2403
154
0.183
2773
X-RAY DIFFRACTION
93.34
1.67-1.71
0.241
136
0.1797
3023
X-RAY DIFFRACTION
96.81
1.71-1.74
0.2104
165
0.1705
2907
X-RAY DIFFRACTION
97.77
1.74-1.78
0.2168
141
0.1734
3016
X-RAY DIFFRACTION
98.41
1.78-1.83
0.2259
155
0.1768
2943
X-RAY DIFFRACTION
97.88
1.83-1.88
0.2345
162
0.1726
2983
X-RAY DIFFRACTION
97.64
1.88-1.93
0.2492
138
0.1777
2898
X-RAY DIFFRACTION
95.92
1.93-2
0.1967
182
0.1709
2917
X-RAY DIFFRACTION
95.77
2-2.06
0.2164
142
0.1722
2353
X-RAY DIFFRACTION
89.04
2.08-2.15
0.2275
123
0.1732
2188
X-RAY DIFFRACTION
92
2.15-2.25
0.2458
149
0.1791
2941
X-RAY DIFFRACTION
96.05
2.25-2.37
0.1965
160
0.1751
2949
X-RAY DIFFRACTION
97.16
2.37-2.51
0.1936
175
0.1868
2904
X-RAY DIFFRACTION
96.01
2.51-2.71
0.2202
167
0.1848
2875
X-RAY DIFFRACTION
95.75
2.71-2.98
0.2244
148
0.1911
2788
X-RAY DIFFRACTION
91.66
2.98-3.41
0.2709
143
0.187
2835
X-RAY DIFFRACTION
93.41
3.41-4.28
0.1894
152
0.1945
2896
X-RAY DIFFRACTION
95.16
4.29-19.39
0.2388
163
0.2285
2812
X-RAY DIFFRACTION
93.29
+
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