Mass: 18.015 Da / Num. of mol.: 229 / 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: 3
-
Sample preparation
Crystal
ID
Density Matthews (Å3/Da)
Density % sol (%)
1
2.85
56.85
2
3
Crystal grow
Temperature (K)
Crystal-ID
Method
pH
Details
277
1
vapor diffusion, sitting drop
7.5
0.2 M magnesium chloride, 30% PEG 400, 0.1 M HEPES, pH 7.5. Additive: 0.002 M manganese chloride, 0.01 M UDP-Galactose
277
2
vapor diffusion, sitting drop
7.5
0.2 M magnesium chloride, 30% PEG 400, 0.1 M HEPES, pH 7.5. Additive: 0.002 M manganese chloride, 0.01 M UDP-Galactose, crystal soaked in higher Mn and UDP-Glc prior to flash cooling.
277
3
vapor diffusion, sitting drop
7.5
0.2 M magnesium chloride, 30% PEG 400, 0.1 M HEPES, pH 7.5. Additive: 0.002 M manganese chloride, 0.01 M UDP-Galactose. Crystal soaked in 1 M NaI prior to flash cooling
-
Data collection
Diffraction
ID
Mean temperature (K)
Crystal-ID
Serial crystal experiment
1
100
1
N
2
100
2
N
3
100
3
N
Diffraction source
Source
Site
Beamline
ID
Wavelength (Å)
SYNCHROTRON
ALS
8.3.1
1
1.1271
SYNCHROTRON
ALS
8.3.1
2
1.1158
SYNCHROTRON
ALS
8.3.1
3
1.7136
Detector
Type
ID
Detector
Date
DECTRIS PILATUS3 6M
1
PIXEL
Jun 2, 2016
DECTRIS PILATUS3 6M
2
PIXEL
Oct 12, 2016
DECTRIS PILATUS3 6M
3
PIXEL
Sep 15, 2016
Radiation
ID
Monochromator
Protocol
Monochromatic (M) / Laue (L)
Scattering type
Wavelength-ID
1
Si(111)
SINGLEWAVELENGTH
M
x-ray
1
2
Si(111)
SINGLEWAVELENGTH
M
x-ray
2
3
Si(111)
SINGLEWAVELENGTH
M
x-ray
3
Radiation wavelength
ID
Wavelength (Å)
Relative weight
1
1.1271
1
2
1.1158
1
3
1.7136
1
Reflection
Biso Wilson estimate: 31.679 Å2 / Entry-ID: 6WFV
Resolution (Å)
Num. obs
% possible obs (%)
Redundancy (%)
CC1/2
Rmerge(I) obs
Rrim(I) all
Χ2
Diffraction-ID
Net I/σ(I)
1.7-41.18
36393
99.7
17.521
0.999
0.117
0.12
0.886
1
19.67
1.96-41.2
22942
96.4
16.4
1
0.037
0.038
2
55.2
2.23-61.5
13578
83.7
29.6
1
0.131
0.134
3
22.8
Reflection shell
Diffraction-ID: 1
Resolution (Å)
Redundancy (%)
Rmerge(I) obs
Mean I/σ(I) obs
Num. measured obs
Num. possible
Num. unique obs
CC1/2
Rrim(I) all
% possible all
1.7-1.74
9.969
1.64
2.1
25451
2649
2553
0.717
1.73
96.4
1.74-1.79
12.41
1.349
3.04
32216
2600
2596
0.869
1.407
99.8
1.79-1.84
16.304
1.088
4.57
41234
2529
2529
0.947
1.123
100
1.84-1.9
19.388
0.868
6.4
47171
2434
2433
0.977
0.891
100
1.9-1.96
19.111
0.681
8.19
45867
2400
2400
0.985
0.7
100
1.96-2.03
18.821
0.495
10.35
43251
2298
2298
0.99
0.508
100
2.03-2.1
18.074
0.42
12.78
40071
2217
2217
0.994
0.433
100
2.1-2.19
19.962
0.358
15.45
42939
2151
2151
0.994
0.367
100
2.19-2.29
20.061
0.285
18.27
41726
2080
2080
0.997
0.292
100
2.29-2.4
19.624
0.215
21.47
38777
1976
1976
0.997
0.221
100
2.4-2.53
18.638
0.194
23
35133
1885
1885
0.997
0.2
100
2.53-2.68
19.732
0.155
27.09
34906
1769
1769
0.996
0.159
100
2.68-2.87
19.698
0.127
30.67
33427
1697
1697
0.998
0.131
100
2.87-3.1
18.617
0.096
35.58
29284
1573
1573
0.998
0.099
100
3.1-3.39
17.244
0.073
39.87
24918
1445
1445
0.999
0.075
100
3.39-3.79
17.841
0.061
46.27
23461
1315
1315
0.999
0.063
100
3.79-4.38
17.107
0.053
49.4
20426
1194
1194
0.999
0.055
100
4.38-5.36
16.239
0.05
49.23
16450
1013
1013
0.999
0.052
100
5.36-7.59
17.028
0.049
49.19
13486
793
792
0.999
0.051
99.9
7.59-41.18
15.608
0.039
50.99
7445
481
477
0.999
0.04
99.2
-
Phasing
Phasing
Method: SIRAS
-
Processing
Software
Name
Version
Classification
PHENIX
1.17.1_3660
refinement
XDS
21-Sep-2016
datareduction
XDS
21-Sep-2016
datascaling
SHELXD
phasing
SOLVE
phasing
RESOLVE
modelbuilding
SHELXE
modelbuilding
Coot
modelbuilding
PDB_EXTRACT
3.25
dataextraction
Refinement
Method to determine structure: SIRAS / Resolution: 1.7→41.18 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 18.31 / Stereochemistry target values: ML
Rfactor
Num. reflection
% reflection
Rfree
0.1722
1931
5.48 %
Rwork
0.1516
33280
-
obs
0.1528
35211
96.48 %
Solvent computation
Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
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