A tetrameric multimer representing the known biologically significant oligomerization state of the molecule cannot be generated by symmetry within the crystal.
Mass: 18.015 Da / Num. of mol.: 111 / Source method: isolated from a natural source / Formula: H2O
Sequence details
THE PROTEIN CRYSTALLIZED IS THE EXTRACELLULAR LIGAND BINDING DOMAIN OF GLUK3. TRANSMEMBRANE REGIONS ...THE PROTEIN CRYSTALLIZED IS THE EXTRACELLULAR LIGAND BINDING DOMAIN OF GLUK3. TRANSMEMBRANE REGIONS WERE GENETICALLY REMOVED AND REPLACED WITH A GLY-THR LINKER (RESIDUES 119 AND 120 OF THE STRUCTURE). THEREFORE, THE SEQUENCE MATCHES DISCONTINUOUSLY WITH THE REFERENCE DATABASE (432-546, 669-806)
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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: 2.56 Å3/Da / Density % sol: 52 %
Crystal grow
Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.2 Details: 1.8 M SODIUM/POTASSIUM PHOSPHATE, CRYSTALS GROWN IN PRESENCE OF GLUTAMATE SOAKED WITH KAINATE, pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution: 2.3501→48.478 Å / Occupancy max: 1 / Occupancy min: 0.38 / SU ML: 0.28 / Isotropic thermal model: Isotropic / σ(F): 1.38 / Phase error: 21.05 / Stereochemistry target values: ML Details: RESIDUES 1-4 (GPGT) WERE NOT LOCATED IN THE ELECTRON DENSITY MAP.
Rfactor
Num. reflection
% reflection
Rfree
0.2322
655
4.95 %
Rwork
0.179
-
-
obs
0.1816
13243
99.98 %
Solvent computation
Shrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.155 Å2 / ksol: 0.378 e/Å3
Displacement parameters
Biso mean: 41.9 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-0.8275 Å2
-0 Å2
0 Å2
2-
-
-0.8275 Å2
0 Å2
3-
-
-
1.655 Å2
Refinement step
Cycle: LAST / Resolution: 2.3501→48.478 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
2019
0
19
111
2149
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
X-RAY DIFFRACTION
f_bond_d
0.012
2110
X-RAY DIFFRACTION
f_angle_d
1.062
2829
X-RAY DIFFRACTION
f_dihedral_angle_d
15.389
795
X-RAY DIFFRACTION
f_chiral_restr
0.072
313
X-RAY DIFFRACTION
f_plane_restr
0.004
358
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
2.3501-2.5315
0.2859
150
0.2041
2432
X-RAY DIFFRACTION
100
2.5315-2.7863
0.2783
118
0.2062
2462
X-RAY DIFFRACTION
100
2.7863-3.1894
0.2796
130
0.1868
2482
X-RAY DIFFRACTION
100
3.1894-4.018
0.1943
127
0.1711
2530
X-RAY DIFFRACTION
100
4.018-48.4881
0.2106
130
0.1665
2682
X-RAY DIFFRACTION
100
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
1.9789
-1.0342
-0.1035
1.6697
0.2731
4.1322
0.0828
0.1122
-0.0206
-0.2438
0.0499
-0.0276
0.1739
0.1347
-0.1101
0.1223
-0.0038
-0.0429
0.1023
0.012
0.1157
-12.8857
44.1079
-21.194
2
0.8699
0.2228
0.007
0.7523
0.6666
0.8396
0.0156
-0.0084
-0.3695
0.3566
0.2205
-0.5476
0.488
0.4039
-0.0334
0.2245
0.2222
-0.2063
0.1228
-0.0578
0.293
-2.3983
26.2034
-14.5059
3
4.2688
4.6871
0.6279
5.5665
0.2475
3.4108
0.0324
-0.5204
0.4785
0.3856
0.0005
0.0752
-0.1814
-0.1286
-0.0348
0.273
0.0899
-0.1226
0.2589
-0.1007
0.2101
-11.2169
46.2037
-2.6061
4
0.8677
-1.7205
-0.3708
3.4557
0.6184
0.4793
0.0045
0.0151
-0.4281
0.6154
-0.0631
0.8527
0.7162
-0.4188
0.2228
0.3054
-0.12
-0.0034
0.2251
0.0235
0.2494
-22.5332
31.7921
-13.0781
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Selection details
1
X-RAY DIFFRACTION
1
chain 'A' and (resseq5:49)
2
X-RAY DIFFRACTION
2
chain 'A' and (resseq50:225)
3
X-RAY DIFFRACTION
3
chain 'A' and (resseq226:241)
4
X-RAY DIFFRACTION
4
chain 'A' and (resseq242:258)
+
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