CRYSTAL PACKING ANALYSIS SUGGESTS THE ASSIGNMENT OF A TETRAMER AS THE SIGNIFICANT OLIGOMERIC FORM IN SOLUTION. ANALYTICAL SIZE-EXCLUSION CHROMATOGRAPHY COUPLED WITH STATIC LIGHT SCATTERING SUGGESTS A HEXAMER AS THE SOLUTION STATE OLIGOMERIC FORM.
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Components
-
Protein , 1 types, 2 molecules AB
#1: Protein
PeptidaseM14, carboxypeptidaseA
Mass: 44758.582 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Shewanella denitrificans (bacteria) / Strain: OS217 / ATCC BAA-1090 / DSM 15013 / Gene: Sden_1905 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q12MY8
Monochromator: Single crystal Si(111) bent monochromator (horizontal focusing) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.97854 Å / Relative weight: 1
Reflection
Resolution: 2.39→49.147 Å / Num. obs: 38954 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 40.987 Å2 / Rmerge(I) obs: 0.206 / Net I/σ(I): 13.16
Reflection shell
Resolution (Å)
Rmerge(I) obs
Mean I/σ(I) obs
Num. measured obs
Num. unique obs
Diffraction-ID
% possible all
2.39-2.48
0.013
2.5
50292
3905
1
98.9
2.48-2.57
0.013
3.2
49078
3418
1
99.7
2.57-2.69
0.013
3.7
56220
3912
1
99.8
2.69-2.83
0.013
5
53968
3768
1
99.7
2.83-3.01
0.013
6.4
55852
3904
1
99.7
3.01-3.24
0.013
9.4
54097
3801
1
99.7
3.24-3.57
0.013
14.5
55526
3934
1
100
3.57-4.08
0.013
21.3
54750
3920
1
100
4.08-5.12
0.013
29.6
54584
3975
1
100
5.12-49.147
0.013
31.7
55863
4417
1
99.5
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Phasing
Phasing
Method: SAD
-
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
SHELXD
phasing
autoSHARP
phasing
Refinement
Method to determine structure: SAD / Resolution: 2.39→49.147 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.922 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 15.453 / SU ML: 0.157 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.31 / ESU R Free: 0.231 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.CALCIUM (CA) HAS BEEN MODELED AT THE PUTATIVE ACTIVE SITE BASED ON ITS PRESENCE AS A CO-CRYSTALLIZATION COMPOUND AND A FLUORESCENCE BASED THERMAL SHIFT BINDING ASSAY. 5.AN UNIDENTIFIED LIGAND (UNL) RESEMBLING GLUTAMIC OR ASPARTIC ACID HAS BEEN MODELED AT THE PUTATIVE ACTIVE SITE. 6.ACETATE (ACT) AND GLYCEROL (GOL) FROM THE CRYSTALLIZATION SOLUTION HAVE BEEN MODELED IN THE SOLVENT STRUCTURE. 7.RAMACHANDRAN OUTLIERS AT RESIDUE 37 IN BOTH CHAINS ARE SUPPORTED BY ELECTRON DENSITY.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.233
1947
5 %
RANDOM
Rwork
0.18
-
-
-
obs
0.182
38841
99.86 %
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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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