Mass: 18.015 Da / Num. of mol.: 214 / 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
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Sample preparation
Crystal
Density Matthews: 2.69 Å3/Da / Density % sol: 54.24 % Description: DATA WERE SCALED USING XSCALE WITH FRIEDEL PAIRS KEPT AS SEPARATE WHEN COMPUTING R-SYM, COMPLETENESS AND
Resolution: 1.95→28.105 Å / Num. obs: 28686 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Redundancy: 3.65 % / Biso Wilson estimate: 20.319 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 8.45
Reflection shell
Resolution (Å)
Rmerge(I) obs
Mean I/σ(I) obs
Num. measured obs
Num. unique obs
Diffraction-ID
% possible all
1.95-2.02
0.499
1.6
10188
5339
1
97.2
2.02-2.1
0.349
2.2
10291
5375
1
98.8
2.1-2.2
0.261
3
11021
5723
1
99
2.2-2.31
0.212
3.7
9929
5147
1
98.9
2.31-2.46
0.173
4.4
10766
5592
1
99.1
2.46-2.65
0.132
5.8
10510
5427
1
98.9
2.65-2.91
0.095
8
10325
5308
1
99
2.91-3.33
0.062
11.6
10490
5400
1
98.5
3.33-4.19
0.036
19.3
10548
5407
1
98.3
4.19-28.105
0.026
24.8
10569
5418
1
97.8
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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
XDS
datareduction
SHARP
phasing
Refinement
Method to determine structure: MAD / Resolution: 1.95→28.105 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.944 / Occupancy max: 1 / Occupancy min: 0.2 / SU B: 5.481 / SU ML: 0.083 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.125 / ESU R Free: 0.122 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS OTHER REFINEMENT REMARKS: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3.A MET- ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS OTHER REFINEMENT REMARKS: 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.DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE (NDP) AND SODIUM (NA), MOST LIKELY BOUND DURING PROTEIN EXPRESSION WERE MODELED INTO THE STRUCTURE. THE SODIUM WAS ASSIGNED BASED ON THE COORDINATION ENVIRONMENT, AGREEMENT WITH ELECTRON DENSITY AND IT STRUCTURAL HOMOLOG(PDB ID 1EBU). ETHYLENE GLYCOL (EDO) USED AS CRYOPROTECTANT WAS MODELED INTO THE STRUCTURE. 5.THE RAMACHANDRAN OUTLIER (GLY146) IS SUPPORTED BY ELECTRON DENSITY.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.193
1435
5 %
RANDOM
Rwork
0.152
-
-
-
obs
0.154
28657
99.6 %
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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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