Mass: 29400.699 Da / Num. of mol.: 2 / Fragment: residues 429-544, 667-806 / Mutation: K696R, I780L, Q784K Source method: isolated from a genetically manipulated source Details: The K665R I749L and Q753K mutations were created intentionally. The 1st residue is a vector encoded affinity tag fragment. Residues 398-513 and 636-775 are cou pled by a synthetic GT peptide. ...Details: The K665R I749L and Q753K mutations were created intentionally. The 1st residue is a vector encoded affinity tag fragment. Residues 398-513 and 636-775 are cou pled by a synthetic GT peptide. The numbering is for the mature protein after cl eavage of the 31 AA signal peptide. Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: GriK2 / Plasmid: pET22B modified / Production host: Escherichia coli (E. coli) / Strain (production host): OrigamiB (DE3) / References: UniProt: P42260
Resolution: 1.5→1.55 Å / Redundancy: 2.4 % / Mean I/σ(I) obs: 1.02 / % possible all: 94
-
Processing
Software
Name
Version
Classification
HKL-2000
datacollection
PHENIX
(phenix.refine)
refinement
HKL-2000
datareduction
HKL-2000
datascaling
Refinement
Method to determine structure: FOURIER SYNTHESIS / Resolution: 1.5→29.525 Å / SU ML: 0.17 / Isotropic thermal model: ISOTROPIC AND TLS / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ML Details: Refinement was started with Refmac_5.2. The final rounds of refinement were performed with phenix and included occupancy refinement for ions, and for residues with alternative conformations.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.1764
4201
5 %
RANDOM
Rwork
0.1474
-
-
-
all
0.1489
83975
-
-
obs
0.1489
83975
97.85 %
-
Solvent computation
Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.754 Å2 / ksol: 0.41 e/Å3
Refinement step
Cycle: LAST / Resolution: 1.5→29.525 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
8663
0
38
721
9422
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
X-RAY DIFFRACTION
f_bond_d
0.01
8822
X-RAY DIFFRACTION
f_angle_d
1.125
16050
X-RAY DIFFRACTION
f_chiral_restr
0.093
665
X-RAY DIFFRACTION
f_plane_restr
0.006
1333
X-RAY DIFFRACTION
f_dihedral_angle_d
14.302
2284
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
1.5-1.517
0.2801
129
0.2068
2458
X-RAY DIFFRACTION
93
1.517-1.5349
0.2407
124
0.1963
2583
X-RAY DIFFRACTION
94
1.5349-1.5536
0.2119
125
0.1856
2609
X-RAY DIFFRACTION
96
1.5536-1.5733
0.2173
132
0.1797
2619
X-RAY DIFFRACTION
97
1.5733-1.594
0.1904
136
0.178
2629
X-RAY DIFFRACTION
97
1.594-1.6158
0.2248
137
0.1709
2681
X-RAY DIFFRACTION
99
1.6158-1.6389
0.2081
133
0.1708
2754
X-RAY DIFFRACTION
99
1.6389-1.6634
0.2233
135
0.1649
2699
X-RAY DIFFRACTION
100
1.6634-1.6893
0.1783
150
0.162
2690
X-RAY DIFFRACTION
99
1.6893-1.717
0.184
117
0.1552
2698
X-RAY DIFFRACTION
99
1.717-1.7466
0.2134
152
0.1492
2699
X-RAY DIFFRACTION
100
1.7466-1.7784
0.1726
142
0.1457
2704
X-RAY DIFFRACTION
99
1.7784-1.8126
0.1814
143
0.144
2678
X-RAY DIFFRACTION
99
1.8126-1.8496
0.1671
150
0.1437
2692
X-RAY DIFFRACTION
99
1.8496-1.8898
0.1897
151
0.1453
2672
X-RAY DIFFRACTION
99
1.8898-1.9338
0.1752
160
0.138
2692
X-RAY DIFFRACTION
99
1.9338-1.9821
0.1641
120
0.1386
2723
X-RAY DIFFRACTION
99
1.9821-2.0357
0.1741
150
0.1285
2651
X-RAY DIFFRACTION
99
2.0357-2.0956
0.1554
133
0.1297
2692
X-RAY DIFFRACTION
99
2.0956-2.1632
0.1617
147
0.122
2662
X-RAY DIFFRACTION
99
2.1632-2.2405
0.1413
138
0.1234
2689
X-RAY DIFFRACTION
98
2.2405-2.3301
0.1485
137
0.1272
2672
X-RAY DIFFRACTION
98
2.3301-2.4361
0.18
165
0.142
2654
X-RAY DIFFRACTION
98
2.4361-2.5645
0.1654
140
0.1427
2656
X-RAY DIFFRACTION
98
2.5645-2.7251
0.1864
141
0.1427
2671
X-RAY DIFFRACTION
98
2.7251-2.9353
0.1923
151
0.1526
2644
X-RAY DIFFRACTION
98
2.9353-3.2304
0.178
143
0.1408
2641
X-RAY DIFFRACTION
97
3.2304-3.6971
0.1532
153
0.1279
2637
X-RAY DIFFRACTION
96
3.6971-4.655
0.138
148
0.1184
2605
X-RAY DIFFRACTION
96
4.655-29.5311
0.1631
119
0.1575
2620
X-RAY DIFFRACTION
94
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
0.5863
0.2929
0.0295
1.0006
-0.0365
0.7176
-0.0429
0.0684
0.0821
-0.1634
0.057
0.0485
-0.0765
0.0013
-0.0181
0.0978
-0.0006
0.0073
0.066
0.0201
0.0768
14.0503
27.9619
-3.0498
2
0.7063
0.2366
0.0432
1.1252
0.4205
0.752
0.0227
-0.0178
0.0669
0.062
-0.0062
-0.1023
-0.0104
0.0425
-0.0223
0.0676
-0.0005
0.0079
0.0504
-0.0074
0.0713
24.3975
33.8104
17.3512
3
0.1076
0.2781
0.0612
0.6786
-0.2225
0.1469
-0.0349
0.126
0.0016
-0.1513
0.047
-0.0545
0.0371
0.0187
0.0028
0.0882
-0.0038
0.0118
0.0746
-0.0034
0.0777
16.474
15.4205
-1.1179
4
1.0525
-0.0122
-0.1896
0.6432
0.0739
0.5234
0.0097
-0.0533
-0.0673
0.0145
0.0144
0.0593
0.0192
-0.0473
-0.0198
0.039
-0.0016
-0.01
0.0536
0.0114
0.0498
5.1805
0.6246
16.7495
5
1.1055
-0.2387
0.074
0.5799
-0.1066
0.801
0.0279
0.0018
-0.0708
-0.0067
-0.0354
-0.0528
0.0645
0.0735
0.0062
0.0412
0.0068
-0.0003
0.0533
0.0003
0.0536
27.7589
-4.7161
11.3192
6
0.4911
0.0651
0.0231
0.6111
-0.2838
0.5225
0.0262
-0.0477
0.0902
0.0711
0.0172
0.0487
-0.0831
-0.0063
-0.0457
0.054
0.0044
0.0051
0.0595
-0.0017
0.0646
7.5992
13.4435
16.9761
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Selection details
1
X-RAY DIFFRACTION
1
chainAand (resid3:108)
2
X-RAY DIFFRACTION
2
chainAand (resid109:216)
3
X-RAY DIFFRACTION
3
chainAand (resid217:252)
4
X-RAY DIFFRACTION
4
chainBand (resid2:108)
5
X-RAY DIFFRACTION
5
chainBand (resid109:216)
6
X-RAY DIFFRACTION
6
chainBand (resid217:252)
+
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