Mass: 18.015 Da / Num. of mol.: 503 / 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 RESIDUES 29-542 OF 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: 2.15 Å3/Da / Density % sol: 42.73 %
Crystal grow
Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.43 Details: NANODROP, 25.0% PEG 3000, 0.1M Sodium acetate pH 4.43, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution: 2.09→29.63 Å / Num. obs: 57418 / % possible obs: 93.2 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 37.054 Å2 / Rmerge(I) obs: 0.041
Reflection shell
Resolution (Å)
Rmerge(I) obs
Mean I/σ(I) obs
Num. measured obs
Num. unique obs
Diffraction-ID
% possible all
2.09-2.16
0.403
2
15496
8398
1
77.9
2.16-2.25
0.308
2.6
21522
11392
1
94.3
2.25-2.35
0.248
3.3
20216
10541
1
93.6
2.35-2.48
0.183
4.4
22485
11577
1
95.2
2.48-2.63
0.145
5.6
20883
10657
1
95.3
2.63-2.83
0.095
8.4
21461
10874
1
95.7
2.83-3.12
0.066
11.6
22267
11255
1
95.1
3.12-3.57
0.038
18.5
21634
10922
1
94.9
3.57-4.49
0.021
30
21501
10867
1
94.4
4.49-29.63
0.017
35.2
21847
11056
1
94.8
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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
SHELX
phasing
MolProbity
3beta29
modelbuilding
XSCALE
datascaling
PDB_EXTRACT
3.006
dataextraction
MAR345
CCD
datacollection
XDS
datareduction
autoSHARP
phasing
SHELXD
phasing
Refinement
Method to determine structure: MAD / Resolution: 2.09→29.63 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.958 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 8.666 / SU ML: 0.117 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.21 / ESU R Free: 0.166 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. ACETATE (ACT) AND GLYCEROL MOLECULES (GOL) FROM THE CRYSTALLIZATION/CRYO SOLUTION WERE MODELED INTO THE STRUCTURE. 5. ELECTRON DENSITY MAPS SUPPORT THE MODELING OF CYS 364 ON THE A AND B SUBUNITS IN A MODIFIED FORM, CYSTEINESULFONIC ACID (OCS).
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.198
2934
5.1 %
RANDOM
Rwork
0.156
-
-
-
obs
0.158
57418
97.27 %
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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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