Mass: 18.015 Da / Num. of mol.: 71 / Source method: isolated from a natural source / Formula: H2O
Sequence details
THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE. THE DNA SEQUENCING OF THE CLONED CONSTRUCT SHOWS A LEUCINE AT POSITION 127 INSTEAD OF A VALINE. THE LEUCINE AT POSITION 127 IS SUPPORTED BY THE ELECTRON DENSITY.
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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: 2.29 Å3/Da / Density % sol: 46.25 %
Crystal grow
Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 31.0% 2-methyl-2,4-pentanediol, 0.2M sodium chloride, 0.1M TRIS pH 7.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 13, 2008 / Details: Flat mirror (vertical focusing)
Radiation
Monochromator: Single crystal Si(111) bent monochromator (ho rizontal focusing) Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
ID
Wavelength (Å)
Relative weight
1
0.97968
1
2
0.97917
1
3
0.91837
1
Reflection
Resolution: 2.5→29.074 Å / Num. obs: 15426 / % possible obs: 93.6 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 49.009 Å2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 11.12
Reflection shell
Resolution (Å)
Highest resolution (Å)
Rmerge(I) obs
Mean I/σ(I) obs
Num. measured obs
Num. unique obs
% possible all
2.5-2.59
0.352
2.3
3928
2486
81.3
2.59-2.69
0.298
2.8
4363
2653
88.6
2.69-2.81
0.212
3.9
4633
2739
91.1
2.81-2.96
0.156
5.2
5084
2897
92.5
2.96-3.15
0.118
6.7
5392
2959
95.1
3.15-3.39
0.071
10.3
5569
2949
96.2
3.39-3.73
0.047
14.2
5738
2989
97.2
3.73-4.26
0.033
18.5
5766
2981
98
4.26-5.35
0.029
21.1
5855
3032
98.4
5.35
0.027
22.5
5933
3064
97.2
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Phasing
Phasing
Method: MAD
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Processing
Software
Name
Version
Classification
NB
REFMAC
5.2.0019
refinement
PHENIX
refinement
SOLVE
phasing
MolProbity
3beta29
modelbuilding
XSCALE
datascaling
PDB_EXTRACT
3.004
dataextraction
XDS
datareduction
Refinement
Method to determine structure: MAD / Resolution: 2.5→29.074 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.898 / SU B: 11.675 / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.691 / ESU R Free: 0.324 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 THE ...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 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.277
772
5 %
RANDOM
Rwork
0.241
-
-
-
obs
0.243
15414
97.85 %
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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: BABINET MODEL WITH MASK
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