Mass: 18.015 Da / Num. of mol.: 157 / 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. THE CLONED CONSTRUCT CONTAINS RESIDUES 29-206 OF THE TARGET SEQUENCE. THE STRAIN CLONED, STREPTOCOCCUS MUTANS CLARKE, DIFFERS FROM THE DATABASE STRAIN, STREPTOCOCCUS MUTANS UA159. SEQUENCING OF THE CLONED CONSTRUCT SHOWS AN ISOLUCINE AT POSITION 150 INSTEAD OF A VALINE. THE ISOLUCINE AT POSITION 150 IS SUPPORTED BY THE ELECTRON DENSITY.
-
Experimental details
-
Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
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Sample preparation
Crystal
Density Matthews: 2.08 Å3/Da / Density % sol: 40.74 %
Crystal grow
Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4 Details: 1.0000M LiCl, 20.0000% PEG-6000, 0.1M Citrate pH 4.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution: 1.4→32.634 Å / Num. obs: 32922 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 16.262 Å2 / Rmerge(I) obs: 0.044 / Net I/σ(I): 12.9
Reflection shell
Diffraction-ID: 1
Resolution (Å)
Highest resolution (Å)
Rmerge(I) obs
Mean I/σ(I) obs
Num. measured obs
Num. unique obs
% possible all
1.4-1.45
0.501
2.4
11443
3244
98.8
1.45-1.51
0.342
3.4
11778
3344
99.2
1.51-1.58
0.241
4.8
11677
3315
99.3
1.58-1.66
0.179
6.3
11168
3160
99.9
1.66-1.76
0.131
8.4
11114
3137
99.6
1.76-1.9
0.086
12.1
11971
3392
99.6
1.9-2.09
0.054
17.4
11476
3253
99.6
2.09-2.39
0.043
21.1
11645
3325
99.6
2.39-3.01
0.036
24.3
11760
3333
99.6
3.01
0.028
27.7
11712
3419
98.5
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Phasing
Phasing
Method: MAD
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Processing
Software
Name
Version
Classification
NB
REFMAC
5.4.0067
refinement
PHENIX
refinement
SHELX
phasing
MolProbity
3beta29
modelbuilding
XSCALE
datascaling
PDB_EXTRACT
3.004
dataextraction
XDS
datareduction
SHELXD
AUTOSHARP
phasing
Refinement
Method to determine structure: MAD / Resolution: 1.4→32.634 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.954 / SU B: 2.001 / SU ML: 0.038 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.062 / ESU R Free: 0.064 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.ACETATE ION FROM CRYSTALLIZATION AND ETHYLENE GLYCOL MOLECULES FROM CRYO CONDITION ARE MODELED IN THE STRUCTURE. 5.THERE IS A LONG REGION OF UNMODELED DENSITY NEAR RESIDUE 113 IN THIS STRUCTURE.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.201
1667
5.1 %
RANDOM
Rwork
0.175
-
-
-
obs
0.176
32922
99.37 %
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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
Displacement parameters
Biso mean: 14.513 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-0.67 Å2
0 Å2
0.44 Å2
2-
-
1.29 Å2
0 Å2
3-
-
-
-0.62 Å2
Refinement step
Cycle: LAST / Resolution: 1.4→32.634 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
1250
0
16
157
1423
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.017
0.021
1400
X-RAY DIFFRACTION
r_bond_other_d
0.002
0.02
921
X-RAY DIFFRACTION
r_angle_refined_deg
1.539
1.943
1904
X-RAY DIFFRACTION
r_angle_other_deg
1.419
3
2266
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
6.252
5
186
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
37.638
26.324
68
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
10.884
15
240
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
28.04
15
4
X-RAY DIFFRACTION
r_chiral_restr
0.097
0.2
205
X-RAY DIFFRACTION
r_gen_planes_refined
0.009
0.02
1653
X-RAY DIFFRACTION
r_gen_planes_other
0.003
0.02
276
X-RAY DIFFRACTION
r_mcbond_it
1.714
3
882
X-RAY DIFFRACTION
r_mcbond_other
0.439
3
357
X-RAY DIFFRACTION
r_mcangle_it
2.794
5
1427
X-RAY DIFFRACTION
r_scbond_it
4.214
8
518
X-RAY DIFFRACTION
r_scangle_it
6.491
11
477
LS refinement shell
Resolution: 1.4→1.436 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.282
119
-
Rwork
0.272
2275
-
all
-
2394
-
obs
-
-
98.36 %
Refinement TLS params.
Method: refined / Origin x: 66.6507 Å / Origin y: 23.0335 Å / Origin z: 12.3906 Å
11
12
13
21
22
23
31
32
33
T
-0.0302 Å2
-0.0075 Å2
0.0035 Å2
-
-0.0213 Å2
-0.0141 Å2
-
-
-0.0248 Å2
L
1.1819 °2
-0.4192 °2
-0.1541 °2
-
0.9294 °2
0.0917 °2
-
-
0.4087 °2
S
-0.059 Å °
-0.0055 Å °
0.0228 Å °
-0.0122 Å °
0.0814 Å °
-0.1876 Å °
0.0007 Å °
0.0115 Å °
-0.0225 Å °
+
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