Mass: 18.015 Da / Num. of mol.: 272 / Source method: isolated from a natural source / Formula: H2O
-
Experimental details
-
Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
-
Sample preparation
Crystal
Density Matthews: 2.16 Å3/Da / Density % sol: 49.54 %
Crystal grow
Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: Protein Solution (10 mg/ml MSE protein, 0.05 M NaCl, 0.0003 M TCEP, 0.005 M HEPES pH 5) mixed in a 1:1 ratio with the Well Solution (55% Polypropylene glycol 400, 0.1 M Triethanolamine pH 7. ...Details: Protein Solution (10 mg/ml MSE protein, 0.05 M NaCl, 0.0003 M TCEP, 0.005 M HEPES pH 5) mixed in a 1:1 ratio with the Well Solution (55% Polypropylene glycol 400, 0.1 M Triethanolamine pH 7.5). Cryoprotected with 55% Polypropylene glycol 400, 0.1 M Triethanolamine pH 7.5, vapor diffusion, hanging drop, temperature 277K
Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 8, 2009 / Details: mirrors and beryllium lenses
Radiation
Monochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.97857 Å / Relative weight: 1
Reflection
Redundancy: 5.8 % / Av σ(I) over netI: 18.16 / Number: 173743 / Rmerge(I) obs: 0.093 / Χ2: 1.18 / D res high: 1.8 Å / D res low: 50 Å / Num. obs: 29918 / % possible obs: 95.9
Diffraction reflection shell
Highest resolution (Å)
Lowest resolution (Å)
% possible obs (%)
ID
Rmerge(I) obs
Chi squared
Redundancy
4.44
50
99.6
1
0.05
1.523
5.6
3.52
4.44
100
1
0.051
1.544
6
3.08
3.52
100
1
0.065
1.223
6.1
2.8
3.08
100
1
0.091
1.15
6.1
2.6
2.8
100
1
0.121
1.19
6.1
2.44
2.6
100
1
0.139
1.213
6.1
2.32
2.44
100
1
0.155
1.15
6.1
2.22
2.32
100
1
0.173
1.103
6.1
2.13
2.22
100
1
0.201
1.153
6.1
2.06
2.13
100
1
0.236
1.103
5.9
2
2.06
97.7
1
0.264
1.078
5.8
1.94
2
94.4
1
0.302
1.113
5.5
1.89
1.94
87.4
1
0.355
1.079
5.4
1.84
1.89
82.3
1
0.416
0.922
5.1
1.8
1.84
76.2
1
0.457
0.935
4.8
Reflection
Resolution: 1.79→50 Å / Num. obs: 29918 / % possible obs: 95.9 % / Redundancy: 5.8 % / Biso Wilson estimate: 19.36 Å2 / Rmerge(I) obs: 0.093 / Χ2: 1.182 / Net I/σ(I): 9.5
Reflection shell
Resolution (Å)
Redundancy (%)
Rmerge(I) obs
Num. unique all
Χ2
% possible all
1.79-1.84
4.8
0.457
1557
0.935
76.2
1.84-1.89
5.1
0.416
1673
0.922
82.3
1.89-1.94
5.4
0.355
1795
1.079
87.4
1.94-2
5.5
0.302
1944
1.113
94.4
2-2.06
5.8
0.264
1973
1.078
97.7
2.06-2.13
5.9
0.236
2060
1.103
100
2.13-2.22
6.1
0.201
2074
1.153
100
2.22-2.32
6.1
0.173
2045
1.103
100
2.32-2.44
6.1
0.155
2055
1.15
100
2.44-2.6
6.1
0.139
2081
1.213
100
2.6-2.8
6.1
0.121
2084
1.19
100
2.8-3.08
6.1
0.091
2069
1.15
100
3.08-3.52
6.1
0.065
2121
1.223
100
3.52-4.44
6
0.051
2120
1.544
100
4.44-50
5.6
0.05
2267
1.523
99.6
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Phasing
Phasing
Method: SAD
Phasing MAD set
ID
Highest resolution (Å)
Lowest resolution (Å)
Power acentric
Power centric
Reflection acentric
Reflection centric
ISO_1
1.79
34.46
0
0
26335
3495
ANO_1
1.79
34.46
0.963
0
25799
0
Phasing MAD set shell
ID
Resolution (Å)
Power acentric
Power centric
Reflection acentric
Reflection centric
ISO_1
7.82-34.46
0
0
262
169
ISO_1
5.6-7.82
0
0
520
182
ISO_1
4.59-5.6
0
0
689
180
ISO_1
3.99-4.59
0
0
837
177
ISO_1
3.57-3.99
0
0
954
182
ISO_1
3.26-3.57
0
0
1056
181
ISO_1
3.02-3.26
0
0
1168
183
ISO_1
2.83-3.02
0
0
1260
183
ISO_1
2.67-2.83
0
0
1335
180
ISO_1
2.53-2.67
0
0
1431
189
ISO_1
2.41-2.53
0
0
1504
181
ISO_1
2.31-2.41
0
0
1552
187
ISO_1
2.22-2.31
0
0
1657
176
ISO_1
2.14-2.22
0
0
1715
181
ISO_1
2.07-2.14
0
0
1771
187
ISO_1
2-2.07
0
0
1812
174
ISO_1
1.94-2
0
0
1808
175
ISO_1
1.89-1.94
0
0
1763
159
ISO_1
1.84-1.89
0
0
1677
140
ISO_1
1.79-1.84
0
0
1564
129
ANO_1
7.82-34.46
2.558
0
262
0
ANO_1
5.6-7.82
2.958
0
520
0
ANO_1
4.59-5.6
2.183
0
689
0
ANO_1
3.99-4.59
2.004
0
837
0
ANO_1
3.57-3.99
2.058
0
954
0
ANO_1
3.26-3.57
1.795
0
1056
0
ANO_1
3.02-3.26
1.64
0
1168
0
ANO_1
2.83-3.02
1.352
0
1260
0
ANO_1
2.67-2.83
1.253
0
1335
0
ANO_1
2.53-2.67
1.062
0
1431
0
ANO_1
2.41-2.53
0.917
0
1504
0
ANO_1
2.31-2.41
0.791
0
1552
0
ANO_1
2.22-2.31
0.659
0
1657
0
ANO_1
2.14-2.22
0.54
0
1714
0
ANO_1
2.07-2.14
0.501
0
1765
0
ANO_1
2-2.07
0.437
0
1791
0
ANO_1
1.94-2
0.38
0
1753
0
ANO_1
1.89-1.94
0.362
0
1675
0
ANO_1
1.84-1.89
0.348
0
1538
0
ANO_1
1.79-1.84
0.321
0
1338
0
Phasing MAD set site
ID
Cartn x (Å)
Cartn y (Å)
Cartn z (Å)
Atom type symbol
B iso
Occupancy
1
-0.486
33.124
75.79
SE
23.07
1.26
2
2.311
7.799
49.803
SE
23.1
1.26
3
9.365
64.364
52.514
SE
20.19
1.16
4
8.391
63.876
11.567
SE
25.9
1.2
5
6.923
65.001
24.109
SE
28.19
1.18
6
2.302
39.911
72.979
SE
29.77
1.15
7
3.003
40.029
4.511
SE
29.98
1.16
8
0.822
21.242
32.489
SE
29.57
1.17
9
9.364
13.339
26.409
SE
34.31
1.14
10
8.023
63.663
65.257
SE
21.58
0.96
11
7.279
18.893
5.541
SE
27.62
0.96
12
4.82
63.065
101.723
SE
31.37
1.04
Phasing dm
Method: Solvent flattening and Histogram matching / Reflection: 29829
Phasing dm shell
Resolution (Å)
Delta phi final
FOM
Reflection
7.37-100
67.4
0.796
512
5.81-7.37
60.1
0.868
504
4.99-5.81
62.2
0.882
569
4.44-4.99
57.9
0.91
629
4.04-4.44
62.2
0.901
705
3.73-4.04
57.9
0.899
740
3.48-3.73
60.2
0.892
817
3.28-3.48
65
0.874
852
3.1-3.28
64.1
0.851
908
2.96-3.1
66.8
0.847
947
2.83-2.96
66.6
0.847
999
2.72-2.83
64.8
0.851
1023
2.62-2.72
65.7
0.849
1084
2.53-2.62
68.7
0.828
1099
2.44-2.53
66.6
0.829
1144
2.37-2.44
67.9
0.853
1182
2.3-2.37
69.3
0.838
1211
2.24-2.3
69.3
0.845
1235
2.18-2.24
70.9
0.863
1275
2.13-2.18
71.9
0.859
1316
2.08-2.13
74.2
0.86
1327
2.03-2.08
76.9
0.866
1373
1.99-2.03
78.3
0.873
1344
1.95-1.99
77.4
0.866
1366
1.91-1.95
78.1
0.859
1322
1.88-1.91
76.9
0.836
1280
1.84-1.88
78.7
0.799
1232
1.79-1.84
81
0.76
1834
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Processing
Software
Name
Version
Classification
NB
DENZO
datareduction
SCALEPACK
datascaling
SHARP
phasing
DM
6.1
phasing
PHENIX
refinement
PDB_EXTRACT
3.005
dataextraction
HKL-2000
datacollection
Refinement
Method to determine structure: SAD / Resolution: 1.792→35.113 Å / Occupancy max: 1 / Occupancy min: 0.29 / SU ML: 0.14 / σ(F): 1.34 / Phase error: 20.05 / Stereochemistry target values: ML
Rfactor
Num. reflection
% reflection
Rfree
0.201
1510
5.06 %
Rwork
0.165
-
-
obs
0.167
29830
95.69 %
Solvent computation
Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.54 Å2 / ksol: 0.349 e/Å3
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