Mass: 18.015 Da / Num. of mol.: 168 / 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: 2.31 Å3/Da / Density % sol: 46.69 %
Crystal grow
Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 7% (v/v) 2-methyl-2,4-pentanediol, 20 mM MgCl2, 80 mM spermine tetrahydrochloride, and 60 mM sodium cacodylate at pH 6.5
-
Data collection
Diffraction
Mean temperature: 100 K / Serial crystal experiment: N
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 1 Å / Relative weight: 1
Reflection
Resolution: 1.24→34.36 Å / Num. obs: 19898 / % possible obs: 99.9 % / Redundancy: 10.8 % / CC1/2: 0.999 / Net I/σ(I): 23.2
Reflection shell
Resolution: 1.24→1.26 Å / Redundancy: 8.4 % / Num. unique obs: 996 / CC1/2: 0.785 / % possible all: 100
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Processing
Software
Name
Version
Classification
REFMAC
5.8.0352
refinement
autoPROC
datareduction
autoPROC
datascaling
PHASER
phasing
Refinement
Method to determine structure: SAD / Resolution: 1.24→34.36 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.963 / SU B: 0.89 / SU ML: 0.039 / Cross valid method: FREE R-VALUE / ESU R: 0.05 / ESU R Free: 0.052 Details: Hydrogens have been added in their riding positions
Rfactor
Num. reflection
% reflection
Rfree
0.2227
972
4.885 %
Rwork
0.1971
18926
-
all
0.198
-
-
obs
-
19898
99.905 %
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: 16.356 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0.665 Å2
0 Å2
-0 Å2
2-
-
0.468 Å2
0 Å2
3-
-
-
-1.134 Å2
Refinement step
Cycle: LAST / Resolution: 1.24→34.36 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
0
486
4
168
658
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.012
0.011
544
X-RAY DIFFRACTION
r_bond_other_d
0.002
0.017
268
X-RAY DIFFRACTION
r_angle_refined_deg
3.073
1.795
836
X-RAY DIFFRACTION
r_angle_other_deg
0.495
1.55
636
X-RAY DIFFRACTION
r_chiral_restr
0.17
0.2
94
X-RAY DIFFRACTION
r_gen_planes_refined
0.039
0.02
292
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
88
X-RAY DIFFRACTION
r_nbd_refined
0.153
0.2
27
X-RAY DIFFRACTION
r_symmetry_nbd_other
0.214
0.2
279
X-RAY DIFFRACTION
r_nbtor_refined
0.256
0.2
184
X-RAY DIFFRACTION
r_symmetry_nbtor_other
0.09
0.2
150
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.166
0.2
91
X-RAY DIFFRACTION
r_symmetry_nbd_refined
0.076
0.2
3
X-RAY DIFFRACTION
r_nbd_other
0.138
0.2
27
X-RAY DIFFRACTION
r_symmetry_xyhbond_nbd_refined
0.17
0.2
16
X-RAY DIFFRACTION
r_scbond_it
1.959
1.943
544
X-RAY DIFFRACTION
r_scbond_other
1.958
1.943
544
X-RAY DIFFRACTION
r_scangle_it
2.851
2.946
836
X-RAY DIFFRACTION
r_scangle_other
2.849
2.945
837
X-RAY DIFFRACTION
r_lrange_it
4.527
32.366
806
X-RAY DIFFRACTION
r_lrange_other
3.997
23.371
750
LS refinement shell
Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Rfactor all
Num. reflection all
Fsc free
Fsc work
% reflection obs (%)
WRfactor Rwork
1.24-1.272
0.261
81
0.303
1356
0.3
1438
0.949
0.926
99.9305
0.282
1.272-1.307
0.287
68
0.295
1347
0.295
1416
0.935
0.929
99.9294
0.263
1.307-1.345
0.29
60
0.278
1320
0.279
1380
0.94
0.936
100
0.244
1.345-1.386
0.362
72
0.251
1232
0.256
1304
0.895
0.953
100
0.214
1.386-1.432
0.284
68
0.238
1242
0.241
1310
0.945
0.958
100
0.205
1.432-1.482
0.281
69
0.22
1168
0.224
1238
0.957
0.967
99.9192
0.187
1.482-1.538
0.215
66
0.222
1160
0.221
1226
0.972
0.969
100
0.191
1.538-1.6
0.24
54
0.206
1125
0.207
1180
0.967
0.971
99.9153
0.181
1.6-1.671
0.267
49
0.204
1047
0.207
1101
0.96
0.975
99.5459
0.189
1.671-1.753
0.156
43
0.186
1032
0.184
1075
0.983
0.977
100
0.178
1.753-1.847
0.156
61
0.169
979
0.168
1040
0.983
0.981
100
0.168
1.847-1.959
0.303
41
0.186
929
0.19
970
0.947
0.977
100
0.191
1.959-2.094
0.201
41
0.194
873
0.194
914
0.977
0.974
100
0.204
2.094-2.261
0.265
42
0.206
828
0.209
871
0.947
0.972
99.8852
0.223
2.261-2.475
0.175
30
0.195
757
0.194
787
0.977
0.977
100
0.225
2.475-2.766
0.28
38
0.204
682
0.208
720
0.943
0.972
100
0.238
2.766-3.19
0.281
36
0.204
630
0.208
668
0.947
0.972
99.7006
0.256
3.19-3.899
0.186
20
0.165
527
0.166
547
0.986
0.983
100
0.228
3.899-5.479
0.169
24
0.177
425
0.176
450
0.983
0.979
99.7778
0.24
5.479-34.36
0.218
9
0.22
267
0.22
278
0.971
0.972
99.2806
0.306
+
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