Mass: 18.015 Da / Num. of mol.: 128 / 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.
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Experimental details
-
Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
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Sample preparation
Crystal
Density Matthews: 2.42 Å3/Da / Density % sol: 49.14 %
Crystal grow
Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 40.0000% Ethylene-Glycol, 5.0000% PEG-3000, 0.1M HEPES pH 7.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Monochromator: Double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.97915 Å / Relative weight: 1
Reflection
Resolution: 2.05→29.67 Å / Num. obs: 16032 / % possible obs: 100 % / Redundancy: 4.8 % / Biso Wilson estimate: 34.881 Å2 / Rmerge(I) obs: 0.096 / Rsym value: 0.096 / Net I/σ(I): 10
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
2.05-2.1
4.9
0.765
1.8
5714
1176
0.765
100
2.1-2.16
4.9
0.595
2.3
5428
1118
0.595
100
2.16-2.22
4.8
0.443
3
5340
1106
0.443
100
2.22-2.29
4.8
0.379
3.7
5211
1079
0.379
100
2.29-2.37
4.8
0.306
4.5
5012
1034
0.306
100
2.37-2.45
4.9
0.245
5.6
4824
994
0.245
100
2.45-2.54
4.9
0.213
6.5
4770
983
0.213
100
2.54-2.65
4.8
0.175
7.9
4526
937
0.175
100
2.65-2.76
4.8
0.158
9.1
4348
901
0.158
100
2.76-2.9
4.8
0.133
10.5
4171
868
0.133
100
2.9-3.06
4.8
0.111
12.5
4011
835
0.111
100
3.06-3.24
4.8
0.098
14.4
3763
783
0.098
100
3.24-3.47
4.8
0.089
16.4
3545
741
0.089
100
3.47-3.74
4.8
0.078
18.4
3302
692
0.078
100
3.74-4.1
4.7
0.064
19.7
3062
646
0.064
100
4.1-4.58
4.7
0.06
21.1
2756
591
0.06
100
4.58-5.29
4.6
0.067
22
2373
516
0.067
100
5.29-6.48
4.4
0.077
22.5
1988
453
0.077
100
6.48-9.17
4.2
0.055
23.9
1553
366
0.055
100
9.17-29.67
3.8
0.049
23.2
803
213
0.049
97
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Phasing
Phasing
Method: SAD
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Processing
Software
Name
Version
Classification
NB
REFMAC
5.2.0019
refinement
PHENIX
refinement
SHELX
phasing
MolProbity
3beta29
modelbuilding
SCALA
3.2.5
datascaling
PDB_EXTRACT
3.006
dataextraction
MOSFLM
datareduction
SHELXD
phasing
autoSHARP
phasing
Refinement
Method to determine structure: SAD / Resolution: 2.05→29.67 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.933 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 8.202 / SU ML: 0.117 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.189 / ESU R Free: 0.18 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN 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 RECORDS CONTAIN 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 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. THE MODEL SHOWS TWO RAMACHANDAN OUTLIERS, ARG 32 AND PRO 33. THESE OUTLIERS ARE SITUATED IN A REGION OF DISORDERED ELECTRON DENSITY BETWEEN RESIDUES 32-38. 5. THERE IS UNIDENTIFIED DENSITY FOUND NEAR THE LIGAND BINDING SITE. IT WAS MODELED AS AN UNKNOWN LIGAND (UNL).
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.248
799
5 %
RANDOM
Rwork
0.187
-
-
-
obs
0.19
16004
99.95 %
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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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