Mass: 29864.492 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: The N-terminal Strep-tag II was removed by TEV cleavage. The construct is a C-terminally truncated GriE (1-265). Source: (gene. exp.) Streptomyces sp. DSM 40835 (bacteria) / Gene: griE / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0E3URV8
Mass: 18.015 Da / Num. of mol.: 624 / Source method: isolated from a natural source / Formula: H2O
-
Experimental details
-
Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
-
Sample preparation
Crystal
Density Matthews: 2.38 Å3/Da / Density % sol: 48.33 %
Crystal grow
Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: MORPHEUS (Molecular Dimensions) condition F1: 0.12 M Monosaccharides, 0.1 M Buffer System 1 pH 6.5, 50 % v/v Precipitant Mix 1 co-crystallization with: 10 mM L-leucine, 10 mM alpha- ...Details: MORPHEUS (Molecular Dimensions) condition F1: 0.12 M Monosaccharides, 0.1 M Buffer System 1 pH 6.5, 50 % v/v Precipitant Mix 1 co-crystallization with: 10 mM L-leucine, 10 mM alpha-ketoglutarate, 10 mM DTT, 125.5 mM Tris/HCl and 1 mM 1 mM MnCl2 and 2 mM Na-ascorbate.
Resolution: 1.529→51.91 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.47 Details: Refinement includes refinement of TLS groups & automatic addition of hydrogens in riding positions
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.1734
4026
5.02 %
copied free R flags from substrate complex (5NCI)
Rwork
0.1554
-
-
-
obs
0.1563
80165
94.24 %
-
Solvent computation
Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement step
Cycle: LAST / Resolution: 1.529→51.91 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
4080
0
38
624
4742
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
X-RAY DIFFRACTION
f_bond_d
0.007
4351
X-RAY DIFFRACTION
f_angle_d
0.923
5939
X-RAY DIFFRACTION
f_dihedral_angle_d
15.075
2630
X-RAY DIFFRACTION
f_chiral_restr
0.057
644
X-RAY DIFFRACTION
f_plane_restr
0.008
804
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
1.5287-1.5467
0.2785
150
0.2593
2746
X-RAY DIFFRACTION
100
1.5467-1.5656
0.2679
167
0.2441
2778
X-RAY DIFFRACTION
100
1.5656-1.5854
0.2556
127
0.2344
2762
X-RAY DIFFRACTION
100
1.5854-1.6062
0.2693
147
0.2314
2773
X-RAY DIFFRACTION
100
1.6062-1.6282
0.2327
140
0.2089
2776
X-RAY DIFFRACTION
100
1.6282-1.6515
0.2205
128
0.2082
2820
X-RAY DIFFRACTION
100
1.6515-1.6762
0.217
139
0.1975
2754
X-RAY DIFFRACTION
100
1.6762-1.7024
0.23
151
0.1889
2774
X-RAY DIFFRACTION
100
1.7024-1.7303
0.1998
145
0.1814
2761
X-RAY DIFFRACTION
100
1.7303-1.7601
0.1986
152
0.1751
2764
X-RAY DIFFRACTION
100
1.7601-1.7921
0.198
137
0.1634
2769
X-RAY DIFFRACTION
100
1.7921-1.8266
0.1855
146
0.1639
2765
X-RAY DIFFRACTION
100
1.8266-1.8639
0.156
147
0.1638
2794
X-RAY DIFFRACTION
100
1.8639-1.9044
0.2074
156
0.1723
2606
X-RAY DIFFRACTION
97
1.9044-1.9487
0.1889
69
0.1789
1329
X-RAY DIFFRACTION
96
1.9487-1.9974
0.1866
140
0.1626
2813
X-RAY DIFFRACTION
100
1.9974-2.0514
0.1589
146
0.1595
2732
X-RAY DIFFRACTION
99
2.0514-2.1118
0.2011
48
0.1536
1079
X-RAY DIFFRACTION
39
2.1118-2.18
0.1798
157
0.1472
2774
X-RAY DIFFRACTION
100
2.18-2.2579
0.1593
122
0.1552
1837
X-RAY DIFFRACTION
96
2.2579-2.3483
0.1764
134
0.1484
2438
X-RAY DIFFRACTION
99
2.3483-2.4552
0.1388
145
0.1431
2767
X-RAY DIFFRACTION
100
2.4552-2.5846
0.1659
171
0.1421
2778
X-RAY DIFFRACTION
100
2.5846-2.7465
0.179
147
0.1456
2802
X-RAY DIFFRACTION
100
2.7465-2.9586
0.1665
139
0.1499
2806
X-RAY DIFFRACTION
100
2.9586-3.2563
0.1896
135
0.1566
2793
X-RAY DIFFRACTION
100
3.2563-3.7273
0.1713
141
0.1476
2836
X-RAY DIFFRACTION
100
3.7273-4.6956
0.1319
134
0.1257
2843
X-RAY DIFFRACTION
100
4.6956-51.9395
0.1649
166
0.1584
2870
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
0.157
-0.0084
0.1342
0.3833
0.2491
0.4712
-0.0369
-0.2943
0.0511
0.1933
0.1282
-0.1986
-0.3374
0.1343
0.0002
0.2303
-0.0444
-0.0352
0.3144
0.017
0.2285
173.942
-19.7799
96.125
2
0.5371
-0.7481
-0.7396
1.341
1.4811
1.7167
0.0639
0.486
0.1868
-0.4704
-0.1276
0.1127
-0.809
-0.2925
-0.0653
0.3619
-0.0768
-0.0093
0.3249
0.0948
0.2496
165.5647
-9.9514
74.126
3
0.845
-0.3139
-0.9392
1.5226
-0.2627
1.4108
-0.0867
0.1856
-0.0235
-0.2829
0.0218
-0.0486
-0.1349
-0.0239
-0.001
0.2481
-0.108
0.0053
0.3197
0.0359
0.1862
171.498
-19.3718
74.9026
4
1.744
0.2776
-0.2987
1.4922
-0.5045
1.5334
-0.0596
0.2644
-0.2969
-0.232
-0.0227
-0.2065
0.1927
0.2461
-0.0042
0.2107
-0.0112
0.0395
0.2569
-0.0128
0.2031
169.3093
-30.5596
81.2875
5
0.7199
0.5309
-0.166
0.4223
0.111
0.7359
-0.0279
-0.0552
-0.2228
-0.0894
-0.0091
-0.3322
0.0689
0.2551
0.0013
0.2042
0.0141
0.0248
0.1795
0.012
0.2103
162.8648
-33.992
92.3452
6
1.1922
0.3205
-0.0648
1.8327
-0.4922
1.8566
-0.088
0.1871
-0.0636
-0.134
0.0215
-0.324
-0.1209
0.3892
-0.014
0.1927
-0.0649
0.0476
0.2936
0.0033
0.2141
174.82
-24.3193
79.4162
7
0.6029
-0.2216
0.0349
0.7697
0.0166
0.7029
0.0114
-0.0006
0.0074
-0.014
-0.0392
0.0034
0.035
-0.0808
-0
0.1401
-0.0107
0.008
0.1089
-0.009
0.1273
137.1343
-30.5951
101.4573
8
0.5823
-0.2627
0.2085
0.2898
-0.2459
0.312
0.131
0.3044
-0.06
-0.2508
-0.0552
-0.012
0.3484
-0.0176
0.0021
0.2579
-0.0352
-0.0311
0.1668
-0.0391
0.1644
136.3251
-44.142
85.6945
9
0.9282
0.2753
-0.2154
1.4083
0.0378
0.9549
0.0167
0.0801
0.0676
-0.1356
-0.0436
0.3115
0.028
-0.1479
-0.002
0.1308
-0.0071
-0.0392
0.1359
-0.0091
0.1792
130.6277
-30.6267
92.3229
10
0.6825
0.1479
-0.3824
0.5888
0.5413
0.9069
-0.0008
0.0522
0.132
-0.1814
-0.0007
-0.0291
-0.1472
0.0014
0.0012
0.1735
0.001
-0.0002
0.1305
0.014
0.1478
143.9038
-24.3397
91.7773
11
0.1963
0.1345
-0.1586
0.2658
-0.0451
0.2263
0.0756
0.3467
0.0298
-0.9592
-0.0828
0.2539
-0.1815
-0.1236
0.0012
0.4805
-0.0183
-0.0888
0.3598
-0.0008
0.3054
133.1591
-29.1019
75.3789
12
1.362
0.1808
-0.0536
1.4718
0.1131
0.7489
-0.0127
0.1421
0.0857
-0.1846
-0.0085
0.2722
0.0105
-0.2014
-0.0028
0.1271
0.0014
-0.0325
0.134
0.0039
0.1338
133.6829
-28.923
90.9484
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Selection details
1
X-RAY DIFFRACTION
1
chain 'A' and (resid1through24 )
2
X-RAY DIFFRACTION
2
chain 'A' and (resid25through40 )
3
X-RAY DIFFRACTION
3
chain 'A' and (resid41through85 )
4
X-RAY DIFFRACTION
4
chain 'A' and (resid86through175 )
5
X-RAY DIFFRACTION
5
chain 'A' and (resid176through200 )
6
X-RAY DIFFRACTION
6
chain 'A' and (resid201through262 )
7
X-RAY DIFFRACTION
7
chain 'B' and (resid2through40 )
8
X-RAY DIFFRACTION
8
chain 'B' and (resid41through65 )
9
X-RAY DIFFRACTION
9
chain 'B' and (resid66through133 )
10
X-RAY DIFFRACTION
10
chain 'B' and (resid134through153 )
11
X-RAY DIFFRACTION
11
chain 'B' and (resid154through175 )
12
X-RAY DIFFRACTION
12
chain 'B' and (resid176through262 )
+
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