Mass: 18.015 Da / Num. of mol.: 100 / 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: 2.41 Å3/Da / Density % sol: 48.89 %
Crystal grow
Temperature: 293.15 K / Method: vapor diffusion, sitting drop Details: 20 mM Magnesium chloride, 50 mM MOPS pH 7.0, 2.0 M Ammonium sulfate, 0.5 mM Spermine PH range: 7
-
Data collection
Diffraction
Mean temperature: 98 K / Serial crystal experiment: N
Diffraction source
Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
Resolution: 1.65→28.562 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.91 / SU B: 2.521 / SU ML: 0.084 / Cross valid method: THROUGHOUT / ESU R: 0.133 / ESU R Free: 0.142 Details: Hydrogens have been added in their riding positions
Rfactor
Num. reflection
% reflection
Rfree
0.2816
542
5.294 %
Rwork
0.216
9696
-
all
0.22
-
-
obs
-
10238
87.437 %
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parameters
Biso mean: 15.201 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-0.003 Å2
-0.001 Å2
-0 Å2
2-
-
-0.003 Å2
0 Å2
3-
-
-
0.009 Å2
Refinement step
Cycle: LAST / Resolution: 1.65→28.562 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
0
424
278
100
802
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.021
0.018
787
X-RAY DIFFRACTION
r_bond_other_d
0.029
0.023
354
X-RAY DIFFRACTION
r_angle_refined_deg
2.984
2.288
1198
X-RAY DIFFRACTION
r_angle_other_deg
3.474
2.486
832
X-RAY DIFFRACTION
r_chiral_restr
0.191
0.2
154
X-RAY DIFFRACTION
r_chiral_restr_other
1.62
0.2
22
X-RAY DIFFRACTION
r_gen_planes_refined
0.017
0.021
417
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.023
136
X-RAY DIFFRACTION
r_nbd_refined
0.219
0.2
89
X-RAY DIFFRACTION
r_symmetry_nbd_other
0.24
0.2
447
X-RAY DIFFRACTION
r_nbtor_refined
0.253
0.2
301
X-RAY DIFFRACTION
r_symmetry_nbtor_other
0.263
0.2
198
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.229
0.2
63
X-RAY DIFFRACTION
r_symmetry_nbd_refined
0.1
0.2
14
X-RAY DIFFRACTION
r_nbd_other
0.19
0.2
49
X-RAY DIFFRACTION
r_symmetry_xyhbond_nbd_refined
0.145
0.2
16
X-RAY DIFFRACTION
r_scbond_it
1.955
1.547
787
X-RAY DIFFRACTION
r_scbond_other
1.955
1.557
788
X-RAY DIFFRACTION
r_scangle_it
3.214
2.305
1198
X-RAY DIFFRACTION
r_scangle_other
3.213
2.316
1199
X-RAY DIFFRACTION
r_lrange_it
5.059
13.795
1086
X-RAY DIFFRACTION
r_lrange_other
5.065
13.592
1074
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
1.65-1.693
0.317
10
0.245
348
X-RAY DIFFRACTION
42.5684
1.693-1.739
0.251
13
0.241
394
X-RAY DIFFRACTION
48.8595
1.739-1.79
0.345
18
0.223
471
X-RAY DIFFRACTION
61.5094
1.79-1.845
0.293
34
0.231
584
X-RAY DIFFRACTION
79.6392
1.845-1.905
0.256
29
0.236
705
X-RAY DIFFRACTION
95.8225
1.905-1.972
0.36
36
0.231
693
X-RAY DIFFRACTION
99.4543
1.972-2.046
0.231
35
0.204
678
X-RAY DIFFRACTION
100
2.046-2.13
0.239
42
0.204
639
X-RAY DIFFRACTION
100
2.13-2.225
0.338
42
0.207
611
X-RAY DIFFRACTION
99.6947
2.225-2.333
0.329
37
0.224
589
X-RAY DIFFRACTION
99.523
2.333-2.459
0.259
31
0.226
568
X-RAY DIFFRACTION
100
2.459-2.608
0.303
21
0.246
556
X-RAY DIFFRACTION
100
2.608-2.788
0.374
31
0.26
510
X-RAY DIFFRACTION
100
2.788-3.011
0.382
35
0.225
472
X-RAY DIFFRACTION
99.4118
3.011-3.298
0.312
28
0.219
436
X-RAY DIFFRACTION
97.8903
3.298-3.687
0.276
25
0.2
402
X-RAY DIFFRACTION
98.1609
3.687-4.256
0.169
26
0.168
338
X-RAY DIFFRACTION
97.0667
4.256-5.209
0.219
20
0.156
311
X-RAY DIFFRACTION
99.3994
5.209-7.353
0.232
14
0.196
253
X-RAY DIFFRACTION
99.2565
7.353-28.562
0.269
15
0.272
138
X-RAY DIFFRACTION
87.931
+
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