Mass: 18.015 Da / Num. of mol.: 532 / Source method: isolated from a natural source / Formula: H2O
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Details
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
-
Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
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Sample preparation
Crystal
Density Matthews: 2.17 Å3/Da / Density % sol: 43.25 %
Resolution: 1.45→28.094 Å / Num. obs: 82675 / % possible obs: 99.4 % / Redundancy: 3.6 % / Biso Wilson estimate: 12.706 Å2 / Rmerge(I) obs: 0.091 / Rsym value: 0.091 / Net I/σ(I): 4.669
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
1.45-1.49
3.6
0.655
1.1
21706
5964
0.655
98.3
1.49-1.53
3.6
0.543
1.3
21147
5838
0.543
98.6
1.53-1.57
3.6
0.456
1.6
20637
5695
0.456
98.9
1.57-1.62
3.6
0.394
1.9
20102
5545
0.394
99
1.62-1.67
3.6
0.329
2.2
19577
5381
0.329
99.2
1.67-1.73
3.6
0.272
2.7
18987
5224
0.272
99.3
1.73-1.8
3.6
0.231
3.2
18349
5030
0.231
99.5
1.8-1.87
3.6
0.185
3.9
17824
4888
0.185
99.6
1.87-1.96
3.7
0.144
5.1
17132
4690
0.144
99.7
1.96-2.05
3.7
0.118
6.2
16486
4493
0.118
99.8
2.05-2.16
3.7
0.102
6.7
15827
4290
0.102
99.9
2.16-2.29
3.7
0.092
7.2
14912
4047
0.092
99.9
2.29-2.45
3.7
0.086
7.7
14135
3840
0.086
100
2.45-2.65
3.7
0.075
8.9
13267
3605
0.075
100
2.65-2.9
3.7
0.063
10.5
12096
3288
0.063
100
2.9-3.24
3.7
0.056
11.5
11036
3009
0.056
100
3.24-3.74
3.6
0.052
5.5
9786
2690
0.052
100
3.74-4.59
3.6
0.043
13.8
8281
2296
0.043
100
4.59-6.48
3.5
0.045
13.3
6369
1807
0.045
100
6.48-28.09
3.2
0.044
13.9
3406
1055
0.044
98.6
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Phasing
Phasing
Method: MAD
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Processing
Software
Name
Version
Classification
NB
REFMAC
5.5.0053
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: 1.45→28.094 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.958 / Occupancy max: 1 / Occupancy min: 0.15 / SU B: 2.068 / SU ML: 0.038 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.059 / ESU R Free: 0.061 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. CHLORIDE IONS (CL) FROM THE PROTEIN BUFFER HAVE BEEN MODELED INTO THE SOLVENT STRUCTURE. 5. ACETATE (ACT) AND ETHYLENE GLYCOL (EDO) FROM THE CRYSTALLIZATION/CRYOPROTECTANT SOLUTIONS HAVE BEEN MODELED INTO THE SOLVENT STRUCTURE. 6. ELECTRON DENSITY RESEMBLING CITRATE PLUS AN ADDITIONAL MOIETY HAS BEEN MODELED AT THE PUTATIVE ACTIVE SITE OF EACH MONOMER AS AN UNIDENTIFIED LIGAND (UNL). 7. A FLAVIN MONONUCLEOTIDE (FMN) IS MODELED IN EACH SUBUNIT. THE PLANARITY RESTRAINTS ON THE FMN ISOALLOXAZINE MOIETY WERE RELAXED TO ALLOW BUTTERFLY BENDING ALONG THE N5-N10 VIRTUAL AXIS TO BETTER FIT THE OBSERVED ELECTRON DENSITY. 8. TLS GROUPS WERE ASSIGNED WITH THE AID OF THE TLSMD SERVER.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.17
4131
5 %
RANDOM
Rwork
0.146
-
-
-
obs
0.147
82611
99.3 %
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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: MASK
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