CRYSTAL PACKING AND ANALYTICAL SIZE EXCLUSION CHROMATOGRAPHY ANALYSES SUPPORT THE ASSIGNMENT OF A DIMER AS THE SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION.
Mass: 18.015 Da / Num. of mol.: 621 / Source method: isolated from a natural source / Formula: H2O
Sequence details
THIS CONSTRUCT (1-406) WAS EXPRESSED WITH THE PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...THIS CONSTRUCT (1-406) WAS EXPRESSED WITH THE 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: 2.4 Å3/Da / Density % sol: 48.76 %
Monochromator: Single crystal Si(111) bent monochromator (horizontal focusing) Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
ID
Wavelength (Å)
Relative weight
1
0.91837
1
2
0.97947
1
Reflection
Resolution: 2.15→29.775 Å / Num. obs: 47045 / % possible obs: 100 % / Redundancy: 4.1 % / Biso Wilson estimate: 20.962 Å2 / Rsym value: 0.16 / Net I/σ(I): 7.2
Reflection shell
Diffraction-ID: 1
Resolution (Å)
Redundancy (%)
Rmerge(I) all
Rmerge(I) obs
Mean I/σ(I) obs
Num. measured all
Num. unique all
Rpim(I) all
Rrim(I) all
Rsym value
Net I/σ(I) obs
% possible all
2.15-2.21
4.2
0.723
0.631
2.2
14304
3436
0.349
0.723
0.631
2.2
100
2.21-2.27
4.2
0.626
0.546
1.4
13830
3328
0.303
0.626
0.546
2.6
100
2.27-2.33
4.2
0.521
0.455
1.7
13720
3293
0.251
0.521
0.455
3.1
100
2.33-2.4
4.2
0.513
0.448
1.7
13141
3151
0.248
0.513
0.448
3.1
100
2.4-2.48
4.2
0.457
0.399
1.9
12804
3067
0.221
0.457
0.399
3.6
100
2.48-2.57
4.2
0.4
0.349
2.2
12353
2968
0.193
0.4
0.349
4
100
2.57-2.67
4.2
0.343
0.3
2.5
11908
2858
0.166
0.343
0.3
4.7
100
2.67-2.78
4.2
0.284
0.248
3
11616
2788
0.137
0.284
0.248
5.5
100
2.78-2.9
4.2
0.252
0.22
3.4
10983
2645
0.122
0.252
0.22
6
100
2.9-3.04
4.2
0.2
0.174
4.3
10622
2549
0.097
0.2
0.174
7.3
100
3.04-3.21
4.1
0.17
0.148
5.1
10085
2433
0.082
0.17
0.148
8.3
100
3.21-3.4
4.1
0.129
0.112
6.6
9556
2307
0.063
0.129
0.112
10.4
100
3.4-3.63
4.1
0.117
0.102
7
8915
2155
0.057
0.117
0.102
11.8
100
3.63-3.93
4.1
0.103
0.09
7.8
8409
2038
0.05
0.103
0.09
13.4
100
3.93-4.3
4.1
0.084
0.073
9.4
7616
1863
0.041
0.084
0.073
15.6
100
4.3-4.81
4.1
0.077
0.067
9.6
7023
1717
0.038
0.077
0.067
16
100
4.81-5.55
4
0.079
0.069
10.1
6147
1521
0.039
0.079
0.069
14.4
100
5.55-6.8
4
0.085
0.074
9.6
5156
1300
0.042
0.085
0.074
12.7
100
6.8-9.62
3.9
0.064
0.055
10.2
4004
1034
0.032
0.064
0.055
15.6
100
9.62-29.775
3.6
0.058
0.049
10.8
2110
594
0.031
0.058
0.049
15.5
96.8
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Phasing
Phasing
Method: MAD
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Processing
Software
Name
Version
Classification
NB
REFMAC
5.5.0110
refinement
PHENIX
refinement
SOLVE
phasing
MolProbity
3beta29
modelbuilding
SCALA
3.3.15
datascaling
PDB_EXTRACT
3.006
dataextraction
MOSFLM
datareduction
Refinement
Method to determine structure: MAD / Resolution: 2.15→29.775 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.937 / Occupancy max: 1 / Occupancy min: 0.15 / SU B: 8.014 / SU ML: 0.112 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.171 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORDS CONTAIN SUM OF TLS AND RESIDUAL U FACTORS. 3. WATERS WERE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORDS CONTAIN SUM OF TLS AND RESIDUAL U FACTORS. 3. WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. 4. 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. 5. ELECTRON DENSITY REVEALS RESIDUE LYS-252 TO BE COVALENTLY ATTACHED TO PYRIDOXAL-5'-PHOSPHATE (PLP) VIA A SCHIFF-BASE LINKAGE. THIS COVALENTLY MODIFIED RESIDUE HAS BEEN MODELED AS 2-LYSINE(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL- PYRIDIN-4-YLMETHANE) (LLP). 6. BASED ON THE ADDITIONAL ELECTRON DENSITY SURROUNDING THE CYS-325 SIDE-CHAIN, THIS CYSTEINE HAS BEEN MODELED AS A CYSTEINE-S-DIOXIDE (CSD) IN BOTH CHAINS A AND B. 7. RESIDUES 12-26 OF CHAIN A AND RESIDUES 12-20 OF CHAIN B WERE UNMODELED DUE TO DISORDER AND LACK OF ELECTRON DENSITY IN THESE REGIONS. 8. CHLORIDE (CL) IONS, GLYCEROL (GOL), AND POLYETHYLENE GLYCOL (PEG) FROM THE PURIFICATION, CRYSTALLIZATION, AND CRYOPROTECTANT SOLUTIONS HAVE BEEN MODELED INTO THE SOLVENT STRUCTURE. 9. TLS GROUPS WERE ASSIGNED WITH THE AID OF THE TLSMD SERVER.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.2
2382
5.1 %
RANDOM
Rwork
0.153
-
-
-
obs
0.156
46978
99.99 %
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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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