Mass: 18.015 Da / Num. of mol.: 338 / Source method: isolated from a natural source / Formula: H2O
Sequence details
SEQUENCE THE CONSTRUCT (RESIDUES 20-146) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. ...SEQUENCE THE CONSTRUCT (RESIDUES 20-146) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.
-
Experimental details
-
Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
-
Sample preparation
Crystal
Density Matthews: 2.57 Å3/Da / Density % sol: 52.23 %
Crystal grow
Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 23.8% polyethylene glycol 3000, 0.1M citric acid pH 6.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Aug 7, 2008 / Details: Flat mirror (vertical focusing)
Radiation
Monochromator: Single crystal Si(111) bent monochromator (horizontal focusing) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.97864 Å / Relative weight: 1
Reflection
Resolution: 1.64→29.775 Å / Num. obs: 35714 / % possible obs: 98.4 % / Redundancy: 7.3 % / Biso Wilson estimate: 20.084 Å2 / Rmerge(I) obs: 0.094 / Rsym value: 0.094 / Net I/σ(I): 5.959
Reflection shell
Diffraction-ID: 1
Resolution (Å)
Redundancy (%)
Rmerge(I) obs
Mean I/σ(I) obs
Num. measured all
Num. unique all
Rsym value
% possible all
1.64-1.68
3.8
0.865
0.9
10044
2621
0.865
97.2
1.68-1.73
7
0.791
0.9
17773
2522
0.791
97.3
1.73-1.78
7.7
0.638
1.2
18925
2468
0.638
97.3
1.78-1.83
7.7
0.471
1.6
18383
2397
0.471
97.9
1.83-1.89
7.7
0.37
2
17900
2333
0.37
98
1.89-1.96
7.7
0.286
2.6
17369
2268
0.286
97.8
1.96-2.03
7.7
0.211
3.6
16885
2203
0.211
98.4
2.03-2.12
7.7
0.182
4
16179
2112
0.182
98.4
2.12-2.21
7.7
0.139
5.3
15687
2040
0.139
98.5
2.21-2.32
7.6
0.13
5.3
14767
1931
0.13
98.6
2.32-2.44
7.7
0.111
6.6
14123
1841
0.111
99
2.44-2.59
7.7
0.098
7.3
13473
1753
0.098
98.9
2.59-2.77
7.7
0.09
7.5
12690
1656
0.09
99.1
2.77-2.99
7.6
0.077
9
11886
1555
0.077
99.2
2.99-3.28
7.7
0.065
10.2
10850
1418
0.065
99.5
3.28-3.67
7.6
0.058
11.3
9912
1303
0.058
99.5
3.67-4.23
7.6
0.056
11.2
8638
1135
0.056
99.7
4.23-5.19
7.5
0.048
12.7
7350
976
0.048
99.7
5.19-7.33
7.4
0.06
10.9
5649
760
0.06
99.7
7.33-29.8
7.1
0.056
11.7
3014
422
0.056
97.9
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Phasing
Phasing
Method: SAD
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Processing
Software
Name
Version
Classification
NB
REFMAC
5.4.0069
refinement
PHENIX
refinement
SOLVE
phasing
MolProbity
3beta29
modelbuilding
SCALA
3.2.5
datascaling
PDB_EXTRACT
3.006
dataextraction
MOSFLM
datareduction
Refinement
Method to determine structure: SAD / Resolution: 1.64→29.775 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.949 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 3.741 / SU ML: 0.065 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.096 / ESU R Free: 0.097 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: (1). HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. (2). A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN ...Details: (1). HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. (2). A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. (3). ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. (4). ONE CITRATE (CIT) ION WAS MODELED BASED ON CRYSTALLIZATION AND CONCLUSIVE ELECTRON DENSITY. (5). RAMACHANDRAN OUTLIERS OF LYS 87 IN BOTH A AND B SUBUNITS ARE SUPPORTED BY ELECTRON DENSITY.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.209
1784
5 %
RANDOM
Rwork
0.172
-
-
-
obs
0.174
35686
98.15 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
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