CRYSTAL PACKING ANALYSIS AND ANALYTICAL SIZE-EXCLUSION CHROMATOGRAPHY SUPPORT THE ASSIGNMENT OF A DIMER AS THE SIGNIFICANT OLIGOMERIC FORM IN SOLUTION.
Mass: 18.015 Da / Num. of mol.: 200 / Source method: isolated from a natural source / Formula: H2O
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Details
Sequence details
THIS CONSTRUCT (RESIDUES 1-224) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...THIS CONSTRUCT (RESIDUES 1-224) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.
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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: 2.48 Å3/Da / Density % sol: 50.48 %
Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Dec 3, 2009 / Details: FLAT MIRROR (VERTICAL FOCUSING)
Radiation
Monochromator: SINGLE CRYSTAL SI(111) BENT MONOCHROMATOR (HORIZONTAL FOCUSING) Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
ID
Wavelength (Å)
Relative weight
1
0.91837
1
2
0.97944
1
3
0.97894
1
Reflection
Resolution: 2.2→29.127 Å / Num. obs: 24823 / % possible obs: 97.6 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 30.791 Å2 / Rmerge(I) obs: 0.095 / Net I/σ(I): 8.35
Reflection shell
Diffraction-ID: 1
Resolution (Å)
Highest resolution (Å)
Rmerge(I) obs
Mean I/σ(I) obs
Num. measured obs
Num. unique obs
% possible all
2.2-2.28
0.651
1.6
9434
4849
96.4
2.28-2.37
0.473
2.2
9359
4799
97.7
2.37-2.48
0.425
2.4
9667
4942
97.6
2.48-2.61
0.325
3.1
9287
4750
98.1
2.61-2.77
0.235
4.1
9202
4708
97.7
2.77-2.98
0.17
5.4
9495
4842
98.2
2.98-3.28
0.109
7.9
9426
4826
98.2
3.28-3.76
0.058
13.6
9694
4948
98.1
3.76-4.72
0.035
19.8
9350
4780
97.6
4.72
0.03
23
9572
4903
96.9
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Phasing
Phasing
Method: MAD
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Processing
Software
Name
Version
Classification
NB
SHELX
phasing
REFMAC
5.5.0110
refinement
XSCALE
datascaling
PDB_EXTRACT
3.1
dataextraction
XDS
datareduction
SHELXD
phasing
autoSHARP
phasing
Refinement
Method to determine structure: MAD / Resolution: 2.2→29.127 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.935 / Occupancy max: 1 / Occupancy min: 0.25 / SU B: 10.753 / SU ML: 0.136 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.188 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. 3.ATOM RECORDS CONTAIN SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4.SOLVENTS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. 5.ZINC (ZN), NICKEL (NI) AND IRON (FE) HAVE BEEN MODELED IN THE PUTATIVE ACTIVE SITE AT PARTIAL OCCUPANCIES BASED ON PEAKS IN AN X-RAY FLUORESCENCE EMISSION SPECTRA AND ANOMALOUS DIFFERENCE FOURIER MAPS CALCULATED FROM DIFFRACTION DATA COLLECTED BELOW AND ABOVE THE K-ABSORPTION EDGES FOR THESE METALS. 6.GLYCEROL (GOL) FROM THE CRYSTALLIZATION SOLUTION HAS BEEN MODELED INTO ELECTRON DENSITY AT THE PUTATIVE ACTIVE AND IT MAY BE A SUBSTRATE MIMIC.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.2112
1263
5.1 %
RANDOM
Rwork
0.1644
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-
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obs
0.1667
24753
99.57 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
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