Mass: 18.015 Da / Num. of mol.: 286 / 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.
-
Experimental details
-
Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
-
Sample preparation
Crystal
Density Matthews: 2.1 Å3/Da / Density % sol: 41.3 %
Crystal grow
Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: 5.0000% Glycerol, 19.0000% iso-Propanol, 19.0000% PEG-4000, 0.1M Citrate pH 5.6, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution: 1.76→30.429 Å / Num. obs: 26997 / % possible obs: 99.1 % / Redundancy: 7 % / Biso Wilson estimate: 18.647 Å2 / Rmerge(I) obs: 0.117 / Rsym value: 0.117 / Net I/σ(I): 4.323
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
1.73-1.77
3.6
0.441
1.7
7152
1973
0.441
97.6
1.77-1.82
6.2
0.469
1.5
11804
1911
0.469
98.9
1.82-1.88
7.4
0.41
1.8
13865
1872
0.41
98.9
1.88-1.93
7.5
0.318
2.2
13406
1796
0.318
98.2
1.93-2
7.5
0.274
2.4
13232
1775
0.274
98.6
2-2.07
7.5
0.23
3
12726
1708
0.23
99.2
2.07-2.15
7.4
0.205
3.3
12360
1662
0.205
99.4
2.15-2.23
7.4
0.188
3.7
11821
1589
0.188
99
2.23-2.33
7.4
0.167
4
11333
1528
0.167
99
2.33-2.45
7.4
0.157
4.3
10850
1467
0.157
99.3
2.45-2.58
7.4
0.133
5.1
10351
1401
0.133
99.5
2.58-2.74
7.4
0.12
5.4
9793
1321
0.12
99.5
2.74-2.92
7.3
0.109
5.9
9257
1261
0.109
99.8
2.92-3.16
7.3
0.095
6.4
8651
1183
0.095
99.9
3.16-3.46
7.3
0.084
7.2
7796
1065
0.084
99.7
3.46-3.87
7.3
0.074
7.7
7178
980
0.074
99.9
3.87-4.47
7.3
0.074
7.8
6201
853
0.074
99.9
4.47-5.47
7.2
0.078
7.3
5340
744
0.078
99.9
5.47-7.74
7
0.082
7.4
4087
580
0.082
100
7.74-30.429
6.4
0.08
6
2107
328
0.08
98.4
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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
SHELXD
phasing
autoSHARP
phasing
Refinement
Method to determine structure: MAD / Resolution: 1.76→30.429 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.936 / Occupancy max: 1 / Occupancy min: 0.38 / SU B: 4.858 / SU ML: 0.081 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.128 / ESU R Free: 0.12 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. GOL MOLECULES FROM THE CRYSTALLIZATION SOLUTION ARE MODELED IN THE PUTATIVE ACTIVE SITE OF THE PROTEIN AND IT MAY REPRESENT THE SUBSTRATE OF THE PROTEIN. 5. THE N-TERMINUS OF CHAIN B SHOWS MULTIPLE ORDER. THIS HAS BEEN MODELED AS TWO CONFORMERS. FOR CONFORMER A, RESIDUES 3-6 HAVE BEEN MODELED WITH RESIDUES 0-2 OMITTED DUE TO DISORDER. FOR CONFORMER B, RESIDUES 1-6 HAVE BEEN MODELED WITH ONLY RESIDUE 0 OMITTED DUE TO DISORDER.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.208
1358
5 %
RANDOM
Rwork
0.17
-
-
-
obs
0.172
26993
98.97 %
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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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