Mass: 18.015 Da / Num. of mol.: 1004 / 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.
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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: 2.33 Å3/Da / Density % sol: 47.15 %
Crystal grow
Temperature: 293 K Details: 20.9000% polyethylene glycol 3350, 0.2360M di-ammonium tartrate, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution: 2→29.775 Å / Num. obs: 120764 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 27.26 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 9.16
Reflection shell
Resolution: 2→2.05 Å / Rmerge(I) obs: 0.676 / Mean I/σ(I) obs: 1.1 / % possible all: 100
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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
XSCALE
datascaling
PDB_EXTRACT
3.006
dataextraction
XDS
datareduction
SCALA
datascaling
SHELXD
phasing
autoSHARP
phasing
Refinement
Method to determine structure: MAD / Resolution: 2→29.77 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.942 / Occupancy max: 1 / Occupancy min: 0.37 / SU B: 8.393 / SU ML: 0.104 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.17 / ESU R Free: 0.149 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: 1). HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS RIDING POSITIONS. 2). ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 3). A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE ...Details: 1). HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 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 THESE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4). ETHYLENE GLYCOL USED AS A CRYOGEN WAS MODELED INTO THE STRUCTURE. 5). IN THE STRUCTURE OF THIS PROTEIN DETERMINED AT LOWER RESOLUTION (PDB ID 3GWP), A BOUND COFACTOR PYRIDOXAL-5'-PHOSPHATE (PLP) AND LYS 243 AT THE ACTIVE SITE WERE MODELED AS N'-PYRIDOXYL-LYSINE-5'-MONOPHOSPHATE (LLP). IN THIS STRUCTURE, A PLP COFACTOR WAS MODELED INTO THE B-SUBUNIT ONLY. SOME OF ELECTRON DENSITIES IN THE VICINITY OF THE ACTIVE SITES ON THE OTHER THREE SUBUNITS WERE MODELED AS L(+)-TARTARIC ACID (TLA), USED AS A BUFFER IN THE CRYSTALLIZATION. 6). ANALYSIS WITH THE MOLPROBITY VALIDATION SERVER SHOWS THAT GLY 380 ON THE A, C, AND D SUBUNITS ARE RAMACHANDRAN OUTLIERS EVEN THOUGH ELECTRON DENSITY SUPPORTS THEIR POSITIONING. 7). ELECTRON DENSITY BETWEEN RESIDUES 369-371 ON THE A SUBUNIT IS DISORDERED AND THESE RESIDUES COULD NOT BE RELIABLY MODELED.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.206
6076
5 %
RANDOM
Rwork
0.165
-
-
-
obs
0.168
120713
99.7 %
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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: MASK
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