Mass: 18.015 Da / Num. of mol.: 531 / Source method: isolated from a natural source / Formula: H2O
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Experimental details
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Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
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Sample preparation
Crystal
Density Matthews: 2.6 Å3/Da / Density % sol: 52.63 %
Crystal grow
Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.5 Details: THE CRYSTAL WAS SOAKED WITH 5mM NAD BEFORE FREEZING. Protein (20 mM Hepes, pH 7.5, 150 mM NaCl, 10% glycerol; Reservoir (0.2M Potassium Chloride, 20% PEG 3350 - MCSG1 #89), Cryoprotection ...Details: THE CRYSTAL WAS SOAKED WITH 5mM NAD BEFORE FREEZING. Protein (20 mM Hepes, pH 7.5, 150 mM NaCl, 10% glycerol; Reservoir (0.2M Potassium Chloride, 20% PEG 3350 - MCSG1 #89), Cryoprotection (Ethylene glycol), Sitting Drop Vapor Diffusion, temperature 298K, VAPOR DIFFUSION, SITTING DROP
Monochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.9793 Å / Relative weight: 1
Reflection
Resolution: 2.1→50 Å / Num. obs: 65989 / % possible obs: 98.6 % / Redundancy: 6.8 % / Biso Wilson estimate: 21.25 Å2 / Rmerge(I) obs: 0.058 / Χ2: 0.855 / Net I/σ(I): 11.7
Reflection shell
Resolution (Å)
Redundancy (%)
Rmerge(I) obs
Num. unique all
Χ2
Diffraction-ID
% possible all
2.1-2.14
5.9
0.182
3114
0.885
1
93.5
2.14-2.18
5.9
0.158
3116
0.861
1
94.3
2.18-2.22
5.9
0.15
3191
0.884
1
95.6
2.22-2.26
5.9
0.143
3234
0.96
1
96.9
2.26-2.31
6
0.123
3259
0.856
1
97.8
2.31-2.37
6.1
0.115
3281
0.849
1
98.6
2.37-2.42
6.3
0.108
3313
0.854
1
99.2
2.42-2.49
6.4
0.109
3305
0.89
1
99.3
2.49-2.56
6.6
0.103
3327
0.93
1
99.6
2.56-2.65
6.8
0.099
3290
0.931
1
99.6
2.65-2.74
6.9
0.089
3361
0.995
1
99.6
2.74-2.85
7.1
0.085
3304
1.011
1
99.8
2.85-2.98
7.2
0.075
3344
1.015
1
99.8
2.98-3.14
7.4
0.067
3345
1.01
1
99.7
3.14-3.33
7.5
0.057
3346
0.895
1
99.9
3.33-3.59
7.6
0.047
3359
0.809
1
100
3.59-3.95
7.6
0.042
3358
0.803
1
100
3.95-4.52
7.6
0.035
3344
0.677
1
99.9
4.52-5.7
7.6
0.032
3394
0.557
1
100
5.7-50
7.4
0.031
3404
0.542
1
98.8
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Phasing
Phasing
Method: SAD
Phasing MAD set site
ID
Cartn x (Å)
Cartn y (Å)
Cartn z (Å)
Atom type symbol
B iso
Occupancy
1
-55.506
-43.71
-26.343
S
20
1
2
-47.66
-29.007
-12.514
S
20
0.96
3
-48.079
-41.674
-42.422
S
20
0.96
4
-67.983
-51.432
3.454
S
20
0.95
5
-37.949
-43.654
-15.784
S
20
0.91
6
-76.484
-36.681
-19.811
S
20
0.88
7
-62.614
-25.856
-16.036
S
20
0.87
8
-71.393
-36.215
-5.345
S
20
0.87
9
-47.29
-28.993
-33.107
S
20
0.87
10
-30.372
-31.089
-10.241
S
20
0.86
11
-60.403
-46.932
-12.232
S
20
0.85
12
-79.978
-21.381
-17.593
S
20
0.85
13
-64.339
-36.215
1.793
S
20
0.85
14
-41.808
-34.516
-27.881
S
20
0.85
15
-39.287
-38.179
-23.614
S
20
0.85
16
-74.082
-36.614
-10.276
S
20
0.84
17
-84.642
-28.044
-28.311
S
20
0.68
18
-46.459
-14.184
-24.324
S
20
0.66
19
-74.828
-53.028
-23.121
S
20
0.62
20
-44.854
-58.552
-21.548
S
20
0.59
21
-60.926
-19.942
1.899
S
20
0.59
22
-61.464
-44.802
13.125
S
20
0.56
23
-28.323
-43.567
-4.819
S
20
0.51
24
-51.855
-29.094
-47.176
S
20
0.43
25
-28.266
-36.579
-32.302
S
20
0.26
26
-85.084
-36.486
-1.014
S
20
0.22
27
-90.953
-41.163
-27.219
S
20
0.22
28
-29.689
-45.873
-31.964
S
20
0.19
29
-96.549
-31.147
0.368
S
20
0.18
30
-92.095
-36.359
-21.257
S
20
0.17
31
-67.339
-53.995
6.068
S
20
0.11
32
-81.512
-26.369
-28.922
S
20
0.1
33
-99.797
-36.751
15.901
S
20
0.09
34
-61.155
-47.258
-16.05
S
20
0.09
35
-44.472
-29.741
-30.875
S
20
0.01
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Processing
Software
Name
Version
Classification
NB
DENZO
datareduction
SCALEPACK
datascaling
SHELX
phasing
PHENIX
1.7.3_928
refinement
PDB_EXTRACT
3.1
dataextraction
CBASS
datacollection
SHELXD
phasing
Refinement
Method to determine structure: SAD / Resolution: 2.096→29.302 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.8805 / SU ML: 0.19 / σ(F): 1.34 / Phase error: 19.09 / Stereochemistry target values: ML Details: PARTIAL NAD DENSITY IS OBSERVED IN ALL 4 MONOMERS AT THE SAME POSITION. ALTHOUGH THIS PARTIAL DENSITY IS SEEN IT IS NOT MODELLED.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.2062
3324
5.04 %
random
Rwork
0.1611
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obs
0.1633
65912
98.49 %
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Solvent computation
Shrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 62.346 Å2 / ksol: 0.4 e/Å3