Mass: 18.015 Da / Num. of mol.: 539 / 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: 2.26 Å3/Da / Density % sol: 45.67 %
Crystal grow
Temperature: 277 K / Method: vapor diffusion, hanging drop Details: Qiagen Cryos Suite #44 (0.09 M HEPES sodium salt pH7.5, 1.26M tri-sodium citrate, 10% (v/v) glycerol) with an extra 2% (v/v) of glycerol.
-
Data collection
Diffraction
Mean temperature: 293 K / Serial crystal experiment: N
Diffraction source
Source: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å
Resolution: 1.76→56.28 Å / SU ML: 0.1978 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.4139 Details: A non-canonical order of axes is used in this structure (P2 21 21)
Rfactor
Num. reflection
% reflection
Rfree
0.2411
5010
4.91 %
Rwork
0.1952
-
-
obs
0.1975
102027
99.87 %
Solvent computation
Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parameters
Biso mean: 35.9 Å2
Refinement step
Cycle: LAST / Resolution: 1.76→56.28 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
7665
0
94
539
8298
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
X-RAY DIFFRACTION
f_bond_d
0.0061
7951
X-RAY DIFFRACTION
f_angle_d
0.7876
10740
X-RAY DIFFRACTION
f_chiral_restr
0.043
1202
X-RAY DIFFRACTION
f_plane_restr
0.0046
1386
X-RAY DIFFRACTION
f_dihedral_angle_d
23.2431
3016
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
1.76-1.78
0.3104
179
0.2493
3133
X-RAY DIFFRACTION
100
1.78-1.8
0.3108
147
0.252
3228
X-RAY DIFFRACTION
100
1.8-1.82
0.29
184
0.2436
3160
X-RAY DIFFRACTION
99.94
1.82-1.85
0.2482
170
0.2274
3200
X-RAY DIFFRACTION
100
1.85-1.87
0.2498
152
0.221
3207
X-RAY DIFFRACTION
99.97
1.87-1.9
0.2847
170
0.2289
3227
X-RAY DIFFRACTION
100
1.9-1.92
0.2868
169
0.2441
3174
X-RAY DIFFRACTION
100
1.92-1.95
0.2864
175
0.2358
3228
X-RAY DIFFRACTION
99.97
1.95-1.98
0.2718
142
0.2336
3202
X-RAY DIFFRACTION
100
1.98-2.01
0.2811
177
0.2137
3224
X-RAY DIFFRACTION
100
2.01-2.05
0.2655
171
0.2167
3169
X-RAY DIFFRACTION
100
2.05-2.09
0.267
155
0.2082
3270
X-RAY DIFFRACTION
100
2.09-2.13
0.2698
176
0.207
3184
X-RAY DIFFRACTION
100
2.13-2.17
0.2769
150
0.1991
3213
X-RAY DIFFRACTION
99.97
2.17-2.22
0.2792
168
0.1965
3226
X-RAY DIFFRACTION
100
2.22-2.27
0.2381
165
0.1951
3250
X-RAY DIFFRACTION
99.97
2.27-2.33
0.2531
177
0.2024
3193
X-RAY DIFFRACTION
99.94
2.33-2.39
0.2384
168
0.2001
3222
X-RAY DIFFRACTION
99.97
2.39-2.46
0.2477
151
0.2121
3240
X-RAY DIFFRACTION
99.88
2.46-2.54
0.2546
160
0.2076
3242
X-RAY DIFFRACTION
99.77
2.54-2.63
0.2807
180
0.2064
3197
X-RAY DIFFRACTION
99.73
2.63-2.73
0.2555
150
0.2112
3246
X-RAY DIFFRACTION
99.5
2.73-2.86
0.2598
169
0.2039
3240
X-RAY DIFFRACTION
99.68
2.86-3.01
0.2615
183
0.2083
3215
X-RAY DIFFRACTION
99.59
3.01-3.2
0.2458
166
0.2066
3273
X-RAY DIFFRACTION
99.74
3.2-3.44
0.2607
151
0.1919
3279
X-RAY DIFFRACTION
99.74
3.44-3.79
0.2091
160
0.1791
3269
X-RAY DIFFRACTION
99.62
3.79-4.34
0.2223
173
0.1582
3299
X-RAY DIFFRACTION
99.66
4.34-5.47
0.1866
188
0.1697
3325
X-RAY DIFFRACTION
99.94
5.47-56.28
0.2134
184
0.1842
3482
X-RAY DIFFRACTION
99.76
+
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