Mass: 18.015 Da / Num. of mol.: 850 / 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 CLONED CONSTRUCT CONTAINS RESIDUES 27-266 OF THE FULL LENGTH PROTEIN.
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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: 2.55 Å3/Da / Density % sol: 51.83 %
Crystal grow
Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 40.0000% Ethanol, 0.1170M magnesium chloride, 0.1M TRIS pH 8.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K
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
0.97926
1
3
0.97882
1
Reflection
Resolution: 2.3→49.507 Å / Num. obs: 186629 / % possible obs: 97.3 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 37.716 Å2 / Rmerge(I) obs: 0.114 / Net I/σ(I): 8.64
Reflection shell
Resolution (Å)
Rmerge(I) obs
Mean I/σ(I) obs
Num. measured obs
Num. unique obs
Diffraction-ID
% possible all
2.3-2.38
0.663
1.8
56759
16841
1
90.9
2.38-2.48
0.576
2.1
64746
18648
1
94.1
2.48-2.59
0.457
2.8
72272
17852
1
96.6
2.59-2.73
0.361
3.8
92657
19108
1
98.4
2.73-2.9
0.271
5
93542
18597
1
98.5
2.9-3.12
0.199
6.8
96338
18467
1
98.9
3.12-3.43
0.129
10.1
101853
18747
1
98.9
3.43-3.93
0.083
14.9
108507
19120
1
98.7
3.93-4.93
0.064
18.6
114186
18929
1
98.8
4.93-49.507
0.061
18.6
137410
20160
1
99.5
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Phasing
Phasing
Method: MAD
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Processing
Software
Name
Version
Classification
NB
REFMAC
5.5.0102
refinement
PHENIX
refinement
SHELX
phasing
MolProbity
3beta29
modelbuilding
XSCALE
datascaling
PDB_EXTRACT
3.006
dataextraction
XDS
datareduction
SHELXD
phasing
autoSHARP
phasing
Refinement
Method to determine structure: MAD / Resolution: 2.3→49.507 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.923 / Occupancy max: 1 / Occupancy min: 0.33 / SU B: 19.051 / SU ML: 0.208 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.411 / ESU R Free: 0.27 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3.A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3.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. 4. ANALYSIS OF THE PATTERSON FUNCTION USING XTRIAGE REVEALS A SIGNIFICANT OFF-ORIGIN PEAK THAT IS 63% OF THE ORIGIN PEAK INDICATING PSEUDO TRANSLATION SYMMETRY RELATING PAIRS OF DIMERS IN THE UNIT CELL. 5.ALTHOUGH THERE IS GENERAL AGREEMENT BETWEEN THE ELECTRON DENSITY MAPS AND THE MODEL MAPS, THE REASONS FOR THE ELEVATED R-FACTORS (R-WORK AND R-FREE) ARE NOT COMPLETELY UNDERSTOOD. 6. GLY 168 ON ALL 16 SUBUNITS IN THE ASYMMETRIC UNIT IS FLAGGED AS A MOLPROBITY RAMACHANDRAN OUTLIER EVEN THOUGH IT IS POSITIONED IN WELL DEFINED ELECTRON DENSITY. HIS A96 IS IN A DISORDERED REGION OF ELECTRON DENSITY AND ARE FLAGGED AS A RAMACHANDRAN OUTLIER IN MOLPROBITY.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.28
9370
5 %
RANDOM
Rwork
0.244
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obs
0.246
186512
97.48 %
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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