Mass: 18.015 Da / Num. of mol.: 192 / Source method: isolated from a natural source / Formula: H2O
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Details
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.
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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
Description: DATA WERE SCALED USING XSCALE WITH FRIEDEL PAIRS KEPT AS SEPARATE WHEN COMPUTING R MERGE, COMPLETENESS AND .
Crystal grow
Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.01M cobalt chloride, 1.8M ammonium sulfate, 0.1M MES pH 6.5, ADDITIVE: 0.001 M S-ADENOSYLMETHIONINE (SAM), NANODROP', VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution: 2.11→30.083 Å / Num. obs: 42096 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 17.9 % / Biso Wilson estimate: 40.16 Å2 / Rmerge(I) obs: 0.221 / Net I/σ(I): 11
Reflection shell
Resolution (Å)
Rmerge(I) obs
Mean I/σ(I) obs
Num. measured obs
Num. unique obs
Diffraction-ID
% possible all
2.11-2.19
1.53
2
64498
8394
1
99.6
2.19-2.27
1.15
2.7
54873
7150
1
99.4
2.27-2.38
0.91
3.5
64861
8442
1
99.7
2.38-2.5
0.67
4.9
58989
7574
1
99.8
2.5-2.66
0.81
6.3
72014
8105
1
99.8
2.66-2.86
0.65
8.4
75514
7751
1
99.8
2.86-3.15
0.53
12.2
87968
7989
1
99.6
3.15-3.6
0.32
17.8
88970
7903
1
99.9
3.6-4.53
0.15
24.2
90866
7956
1
99.8
4.53-30.083
0.09
27.8
93659
8021
1
99.5
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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
SHELXD
phasing
autoSHARP
phasing
Refinement
Method to determine structure: MAD / Resolution: 2.11→30.083 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.967 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 4.175 / SU ML: 0.062 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.095 / ESU R Free: 0.09 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.S-ADENOSYLMETHIONINE WAS ADDED DURING CRYSTALLIZATION. IN THIS STRUCTURE, ONLY S-ADENOSYL-L-HOMOCYSTEINE( SAH) IS MODELED IN THE CONSERVED BINDING SITE DUE TO A POSSIBLE ENZYMATICALLY RELATED DEGRADATION. AN UNKNOWN LIGAND (UNL) IS MODELED NEXT TO THE S-ADENOSYL-L- HOMOCYSTEINE IN THE SAME BINDING SITE. THE SHAPE OF THE LIGAND IS CREATINE LIKE. 5.A COBALT ION FROM THE CRYSTALLIZATION REAGENT IS MODELED IN THIS STRUCTURE. THE PRESENCE OF THE CO ATOM IS SUPPORTED BY X-RAY FLUORESCENCE MEASUREMENTS, ANOMALOUS DIFFERENCE FOURIERS AND GEOMETRY. ADDITIONAL ELECTRON DENSITY IS OBSERVED ADJACENT TO THE COBALT ION AND NEAR TO RESIDUES 203 AND 243. THIS DENSITY WAS LEFT UNMODELED. 6.AN IMIDAZOLE MOLECULE AND CHLORIDE ION FROM THE PROTEIN BUFFER, SULFATE IONS FROM THE CRYSTALLIZATION CONDITION AND ETHYLENE GLYCOL MOLECULES FROM THE CRYOPROTECTANT ARE ALSO MODELED IN THIS STRUCTURE.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.175
2128
5.1 %
RANDOM
Rwork
0.162
-
-
-
obs
0.163
42037
99.77 %
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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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