CRYSTAL PACKING ANALYSIS SUGGESTS THE ASSIGNMENT OF A HEXAMER AS THE SIGNIFICANT OLIGOMERIZATION STATE.
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Components
#1: Protein
putativethioesterase
Mass: 18020.449 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Syntrophus aciditrophicus SB (bacteria) Gene: SYNAS_18640, SYN_01977, YP_461911.1 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q2LUI2
Sequence details
SEQUENCE THIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...SEQUENCE THIS 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
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Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
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Sample preparation
Crystal
Density Matthews: 2.27 Å3/Da / Density % sol: 45.88 %
Crystal grow
Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5 Details: 10.0000% MPD, 0.1M Citrate pH 5.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution: 2.5→29.591 Å / Num. obs: 17799 / % possible obs: 99.9 % / Redundancy: 7.2 % / Biso Wilson estimate: 60.865 Å2 / Rmerge(I) obs: 0.084 / Rsym value: 0.084 / Net I/σ(I): 16.8
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
2.5-2.56
7.3
0.806
2.4
9445
1288
0.806
100
2.56-2.64
7.4
0.641
3.1
9165
1246
0.641
100
2.64-2.71
7.3
0.555
3.5
8999
1226
0.555
100
2.71-2.8
7.3
0.446
4.3
8701
1187
0.446
100
2.8-2.89
7.3
0.325
5.9
8436
1156
0.325
100
2.89-2.99
7.3
0.273
7
8285
1133
0.273
100
2.99-3.1
7.3
0.218
8.9
7836
1069
0.218
100
3.1-3.23
7.3
0.16
11.9
7569
1039
0.16
100
3.23-3.37
7.3
0.132
14.4
7278
1002
0.132
100
3.37-3.54
7.3
0.104
18.1
7067
973
0.104
100
3.54-3.73
7.2
0.078
23.8
6642
919
0.078
100
3.73-3.95
7.2
0.069
26.7
6229
867
0.069
100
3.95-4.23
7.2
0.063
31.4
5967
833
0.063
100
4.23-4.56
7.2
0.053
36.1
5479
766
0.053
100
4.56-5
7.1
0.05
39.1
5055
712
0.05
100
5-5.59
7
0.052
36.8
4578
658
0.052
100
5.59-6.45
6.8
0.063
34.1
4007
586
0.063
100
6.45-7.91
6.5
0.064
35.8
3285
509
0.064
100
7.91-11.18
6.3
0.045
42.2
2503
398
0.045
100
11.18-29.59
5.7
0.043
39.3
1316
232
0.043
93.9
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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
SCALA
3.2.5
datascaling
PDB_EXTRACT
3.006
dataextraction
MOSFLM
datareduction
autoSHARP
phasing
Refinement
Method to determine structure: MAD / Resolution: 2.5→29.591 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.914 / Occupancy max: 1 / Occupancy min: 0.37 / SU B: 23.429 / SU ML: 0.233 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.635 / ESU R Free: 0.296 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.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.257
903
5.1 %
RANDOM
Rwork
0.237
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-
-
obs
0.238
17760
99.89 %
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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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