Mass: 18.015 Da / Num. of mol.: 742 / Source method: isolated from a natural source / Formula: H2O
-
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: 2.36 Å3/Da / Density % sol: 47.8 %
Crystal grow
Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: Internal tracking number 226935D6. The crystallant was JCSG screen condition D6: 30% PEG 8000, 0.1 M Tris 8.5, 200 mM MgCl2. The protein solution was TogoA.17127.a.A1 PW28176 at 26.2 mg/mL ...Details: Internal tracking number 226935D6. The crystallant was JCSG screen condition D6: 30% PEG 8000, 0.1 M Tris 8.5, 200 mM MgCl2. The protein solution was TogoA.17127.a.A1 PW28176 at 26.2 mg/mL in a stabilizing buffer of 500 mM NaCl, 25 mM HEPES, 5% glycerol, 0.025% azide, 2 mM DTT, pH 7.0 with 10mM Glucose-6-phosphate. 0.4 + 0.4 uL sitting drop vapor diffusion. Cryoprotection: 20% ethylene glycol., vapor diffusion, sitting drop, temperature 290K, VAPOR DIFFUSION, SITTING DROP
Resolution: 2.1→50 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.915 / SU B: 8.241 / SU ML: 0.116 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.184 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.219
3415
5.1 %
RANDOM
Rwork
0.171
-
-
-
obs
0.173
67567
96.15 %
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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: 16.471 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0.95 Å2
0 Å2
0 Å2
2-
-
-0.31 Å2
0 Å2
3-
-
-
-0.64 Å2
Refinement step
Cycle: LAST / Resolution: 2.1→50 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
8840
0
41
742
9623
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.012
0.019
9143
X-RAY DIFFRACTION
r_bond_other_d
0.001
0.02
6250
X-RAY DIFFRACTION
r_angle_refined_deg
1.519
1.949
12378
X-RAY DIFFRACTION
r_angle_other_deg
0.951
3
15172
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.87
5
1138
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
33.09
23.547
437
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
13.82
15
1545
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
15.144
15
66
X-RAY DIFFRACTION
r_chiral_restr
0.087
0.2
1348
X-RAY DIFFRACTION
r_gen_planes_refined
0.007
0.021
10248
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
1942
LS refinement shell
Resolution: 2.1→2.154 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.29
184
-
Rwork
0.219
3663
-
all
-
3847
-
obs
-
-
77.8 %
Refinement TLS params.
Method: refined / Refine-ID: X-RAY DIFFRACTION
ID
L11 (°2)
L12 (°2)
L13 (°2)
L22 (°2)
L23 (°2)
L33 (°2)
S11 (Å °)
S12 (Å °)
S13 (Å °)
S21 (Å °)
S22 (Å °)
S23 (Å °)
S31 (Å °)
S32 (Å °)
S33 (Å °)
T11 (Å2)
T12 (Å2)
T13 (Å2)
T22 (Å2)
T23 (Å2)
T33 (Å2)
Origin x (Å)
Origin y (Å)
Origin z (Å)
1
0.3805
0.0629
-0.2496
0.3935
-0.1082
0.3816
-0.002
0.0346
0.067
0.0004
0.0022
0.0407
-0.0354
-0.0504
-0.0002
0.0248
0.0059
-0.0143
0.0212
-0.0094
0.0319
66.309
74.229
20.201
2
0.1337
0.0018
-0.0909
0.3679
0.0041
0.2309
-0.0154
0.0321
0.0081
-0.0121
-0.0061
0.019
-0.0022
-0.0361
0.0215
0.0303
-0.008
-0.0054
0.0362
-0.0169
0.0164
69.284
60.647
21.085
3
0.3497
-0.0197
0.167
0.3217
0.0274
0.9105
-0.0018
0.0482
-0.0702
-0.0424
0.0051
-0.0746
0.0746
0.0252
-0.0032
0.0437
-0.0006
0.0241
0.0096
-0.0147
0.0423
86.293
39.577
13.858
4
0.1569
-0.035
0.0622
0.3066
0.0304
0.2262
-0.0049
0.0267
-0.0203
-0.0238
-0.0133
-0.0418
0.044
0.0033
0.0182
0.0295
-0.008
0.0141
0.0273
-0.0139
0.0206
83.201
51.903
19.255
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Auth asym-ID
Auth seq-ID
1
X-RAY DIFFRACTION
1
A
1 - 183
2
X-RAY DIFFRACTION
2
A
184 - 562
3
X-RAY DIFFRACTION
3
B
5 - 183
4
X-RAY DIFFRACTION
4
B
184 - 562
+
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